Calculate the probability of genotypes based on the product of allele frequencies over all loci.
Arguments
- gid
a genind or genclone object.
- pop
either a formula to set the population factor from the
strataslot or a vector specifying the population factor for each sample. Defaults toNULL.- by_pop
When this is
TRUE(default), the calculation will be done by population.- log
a
logicaliflog =TRUE(default), the values returned will be log(Pgen). Iflog = FALSE, the values returned will be Pgen.- freq
a vector or matrix of allele frequencies. This defaults to
NULL, indicating that the frequencies will be determined via round-robin approach inrraf. If this matrix or vector is not provided, zero-value allele frequencies will automatically be corrected. For details, please see the documentation on correcting rare alleles.- ...
options from correcting rare alleles. The default is to correct allele frequencies to 1/n
Details
Pgen is the probability of a given genotype occuring in a population assuming HWE. Thus, the value for diploids is
$$P_{gen} = \left(\prod_{i=1}^m p_i\right)2^h$$
where \(p_i\) are the allele frequencies and h is the count of the number of heterozygous sites in the sample (Arnaud-Haond et al. 2007; Parks and Werth, 1993). The allele frequencies, by default, are calculated using a round-robin approach where allele frequencies at a particular locus are calculated on the clone-censored genotypes without that locus.
To avoid issues with numerical precision of small numbers, this function calculates pgen per locus by adding up log-transformed values of allele frequencies. These can easily be transformed to return the true value (see examples).
Note
For haploids, Pgen at a particular locus is the allele frequency. This
function cannot handle polyploids. Additionally, when the argument
pop is not NULL, by_pop is automatically TRUE.
References
Arnaud-Haond, S., Duarte, C. M., Alberto, F., & Serrão, E. A. 2007. Standardizing methods to address clonality in population studies. Molecular Ecology, 16(24), 5115-5139.
Parks, J. C., & Werth, C. R. 1993. A study of spatial features of clones in a population of bracken fern, Pteridium aquilinum (Dennstaedtiaceae). American Journal of Botany, 537-544.
Examples
data(Pram)
head(pgen(Pram, log = FALSE))
#> PrMS6A1 Pr9C3A1 PrMS39A1 PrMS45A1 PrMS43A1
#> 1411152-10B 0.5 0.5 0.15 0.5 0.111111111
#> 82 0.5 0.5 0.35 0.5 0.111111111
#> 83 0.5 0.5 0.15 0.5 0.002298851
#> 84 0.5 0.5 0.35 0.5 0.004597701
#> 85 0.5 0.5 0.35 0.5 0.222222222
#> 81-NM-1 0.5 0.5 0.35 0.5 0.111111111
# \dontrun{
# You can also supply the observed allele frequencies
pramfreq <- Pram %>% genind2genpop() %>% tab(freq = TRUE)
#>
#> Converting data from a genind to a genpop object...
#>
#> ...done.
#>
head(pgen(Pram, log = FALSE, freq = pramfreq))
#> PrMS6A1 Pr9C3A1 PrMS39A1 PrMS45A1 PrMS43A1
#> 1411152-10B 0.5 0.5 0.1301308 0.5 0.048799049
#> 82 0.5 0.5 0.3664209 0.5 0.129488704
#> 83 0.5 0.5 0.1301308 0.5 0.011771700
#> 84 0.5 0.5 0.3664209 0.5 0.001355529
#> 85 0.5 0.5 0.3664209 0.5 0.134197384
#> 81-NM-1 0.5 0.5 0.3664209 0.5 0.129488704
# You can get the Pgen values over all loci by summing over the logged results:
pgen(Pram, log = TRUE) %>% # calculate pgen matrix
rowSums(na.rm = TRUE) %>% # take the sum of each row
exp() # take the exponent of the results
#> 1411152-10B 82 83
#> 2.083333e-03 4.861111e-03 4.310345e-05
#> 84 85 81-NM-1
#> 2.011494e-04 9.722222e-03 4.861111e-03
#> 06-1413-1 07-83-7-A ODA-06-1029-82B
#> 4.185268e-03 4.715795e-04 4.185268e-03
#> ODA-06-1029-82C ODA-06-1029-109A ODA-06-1029-109B
#> 4.185268e-03 4.185268e-03 4.185268e-03
#> 118-28-A 08-206-44-B 08-206-44-D
#> 4.185268e-04 1.395089e-03 1.395089e-03
#> 08-206-44-E 351-5-A 351-5-C
#> 1.395089e-03 1.771191e-05 1.771191e-05
#> 351-5-D 351-5-E 04-76-C
#> 1.771191e-05 1.771191e-05 5.580357e-04
#> 04-335-2A 04-189-B4 03-74-N10A-B
#> 4.185268e-03 8.370536e-04 8.370536e-04
#> 05-2033-72 05-2033-73 05-2086-12
#> 4.715795e-04 4.715795e-04 1.395089e-03
#> 05-2086-20 05-2086-31 05-2086-34
#> 4.715795e-04 1.571932e-04 1.395089e-03
#> 05-2088-3 06-30 06-81-2
#> 4.185268e-03 4.185268e-03 1.395089e-03
#> 06-1036-71B 06-1036-71C 06-1029-122D
#> 4.185268e-03 4.185268e-03 4.185268e-03
#> 06-1029-122C 06-1029-122A 06-1029-98C
#> 4.185268e-04 4.185268e-04 1.771191e-05
#> 06-1027-90 1369017-9 1352535-6
#> 4.185268e-03 4.861111e-03 4.861111e-03
#> 1343990-17 1344272-8 1411152-10A
#> 1.005747e-04 4.861111e-03 2.083333e-03
#> 1341321-16 1418983-2 1402871-B
#> 4.161712e-06 1.041667e-03 2.011494e-04
#> 1373915-5 1343990-10 1360295-17
#> 2.011494e-04 4.861111e-03 2.011494e-04
#> 1341321-32 1339849-3 1339849-5
#> 2.011494e-04 4.861111e-03 4.861111e-03
#> 1339849-6 1339849-7 1339849-8
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 1339849-10 1339849-12 1339849-13
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 1339849-15 1339849-16 1339849-17
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 1429425 07-83-7-B 07-83-37-D
#> 4.861111e-03 1.395089e-03 4.185268e-03
#> 07-83-38-B 07-83-38-D 1370431-1
#> 4.185268e-03 4.185268e-04 9.722222e-03
#> 1370431-2 1370431-3 1370431-4
#> 9.722222e-03 2.011494e-04 2.011494e-04
#> 1370431-5 1428631-1 04-278-3
#> 9.722222e-03 1.005747e-04 4.185268e-03
#> 04-335-2B 04-335-2C 1314176-9
#> 4.185268e-03 3.143863e-05 4.861111e-03
#> 1314176-13 1387968 1418886
#> 4.861111e-03 1.005747e-04 2.011494e-04
#> 04-83D Phytr-06-4 Phytr-0-217
#> 5.580357e-04 2.430556e-03 4.861111e-03
#> NOR1.2 MCK1.1 MCK1.2
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 4123.100000000000364 07-1161-1C 07-1161-1E
#> 1.571932e-04 8.370536e-03 4.185268e-03
#> 07-1161-4A 07-1161-4B 07-1161-3-1
#> 4.185268e-03 1.395089e-03 4.185268e-03
#> 07-1161-3-2 07-1161-3-3 07-1161-5A
#> 4.185268e-03 4.185268e-03 1.395089e-03
#> 07-1161-5D 1314070-20 07-1240-1
#> 1.395089e-03 4.861111e-03 4.185268e-03
#> 08-15-1 08-16-1 1368791-19
#> 4.185268e-03 4.185268e-03 2.083333e-03
#> 1368791-21 1429891-1 1429891-2
#> 1.041667e-03 2.083333e-03 8.620690e-05
#> 1429891-3 1429891-4 1429891-6
#> 4.861111e-03 2.083333e-03 2.083333e-03
#> 1429891-7 1429891-10 1429891-11
#> 2.083333e-03 2.083333e-03 2.083333e-03
#> 1437044-28 1454471-29 1454471-31
#> 8.620690e-05 1.783591e-06 1.783591e-06
#> 1309326-1 1480397 1368791-2
#> 4.861111e-03 2.083333e-03 1.005747e-04
#> 1281744-1 1281744-3 1281744-5
#> 2.083333e-03 2.083333e-03 1.041667e-03
#> 1281744-6 1281744-7 1281744-9
#> 2.083333e-03 8.620690e-05 4.166667e-03
#> 1281744-10 1281744-15 1281744-16
#> 2.083333e-03 2.083333e-03 4.166667e-03
#> 1281744-21 1454527-12 1480844-4
#> 2.083333e-03 4.861111e-03 4.861111e-03
#> 1480844-5 1480844-8 1480844-10
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 1281744-4 1480841-6 1281789-1
#> 2.083333e-03 2.083333e-03 2.083333e-03
#> 1281789-2 1431833-31 1431833-32
#> 2.083333e-03 4.861111e-03 4.861111e-03
#> 1431833-39 1309305-21 118-28-B
#> 4.861111e-03 2.011494e-04 4.185268e-03
#> 118-28-E 134-19-E 134-20-E
#> 4.185268e-04 8.370536e-03 4.185268e-03
#> Pr 519- LTR1.2 Pr 520- MCK1.1 09-133-4 ODA
#> 9.722222e-03 4.861111e-03 1.395089e-03
#> SOD OR 10-59-3-A SOD OR 10-59-3-D SOD OR 10-59-3-E
#> 4.185268e-03 4.185268e-03 4.185268e-03
#> SOD OR 10-59-3-F SOD OR 10-59-3-H Pr 731
#> 4.185268e-03 4.185268e-03 5.208333e-04
#> Pr 732 Pr 733 Pr 734
#> 5.208333e-04 1.215278e-03 1.215278e-03
#> Pr 735 1441558-37 1441558-39
#> 1.215278e-03 4.861111e-03 9.722222e-03
#> 1469925-55 1538371-8 1560692-17
#> 1.783591e-06 9.722222e-03 1.340996e-04
#> 1623730-36 1623827-6 1631078-10
#> 9.722222e-03 9.722222e-03 4.861111e-03
#> 1631078-12 #4177 Blomquist back up 1631081-1
#> 9.722222e-03 4.861111e-03 4.861111e-03
#> 1631081-2 1631081-3 1631081-15
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 1631081-17 1631081-22 1644850-1
#> 9.722222e-03 4.861111e-03 9.722222e-03
#> 1644850-2 1644850-4 1644850-5
#> 9.722222e-03 9.722222e-03 9.722222e-03
#> 1644850-6 1644850-7 1644850-8
#> 9.722222e-03 4.861111e-03 9.722222e-03
#> 1644856-18 1644856-35 1341878-7
#> 9.722222e-03 9.722222e-03 8.620690e-05
#> 1341878-49 1365048 1496607
#> 2.083333e-03 2.011494e-04 2.011494e-04
#> 1560191-36 1583329-B 1583329-C
#> 4.161712e-06 2.011494e-04 4.861111e-03
#> 1596853 1596854 1621925-9
#> 9.722222e-03 8.620690e-05 9.722222e-03
#> 1621925-11 1621926-8 1626660-3
#> 9.722222e-03 9.722222e-03 9.722222e-03
#> 1625769 1626651-10 1626656-1
#> 2.011494e-04 9.722222e-03 9.722222e-03
#> 1644994-2 PC#11-1366 ODA 81-8
#> 9.722222e-03 4.861111e-03 1.771191e-05
#> ODA 81-9 ODA 81-37 ODA 114-6
#> 1.771191e-05 1.771191e-05 1.771191e-05
#> 120187 120189 120231
#> 3.143863e-05 4.861111e-03 2.011494e-04
#> 1404252-18 1497058-26 1644623-8
#> 2.011494e-04 8.620690e-05 2.011494e-04
#> 1644623-26 230P06005897-8 230P06005897-9
#> 4.161712e-06 2.011494e-04 2.011494e-04
#> 230P06005898-20 230P06005898-21 10998-V2
#> 2.011494e-04 2.011494e-04 1.571932e-05
#> 1004.1 1008.1 1019.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 1021.1 1030.1 1031.1
#> 3.128552e-05 1.962943e-02 1.962943e-02
#> 1032.1 1033.1 1041
#> 1.962943e-02 1.877131e-04 1.962943e-02
#> 1044 1055 2029.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2043.1 2091.1 2092
#> 1.962943e-02 1.962943e-02 1.673328e-04
#> 2096 2099.1 2108.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2108.2 2110.4 4088.1
#> 1.877131e-04 1.962943e-02 3.271572e-03
#> 4089.1 4120 4122.4
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4131 4143.1 4144.1
#> 1.962943e-02 3.271572e-03 1.962943e-02
#> 4146.1 4154 4158.2
#> 1.962943e-02 3.128552e-05 1.962943e-02
#> 4167.1 4168.2 4169.1
#> 1.877131e-04 1.877131e-04 1.962943e-02
#> 4172.2 4173.2 5013.1
#> 1.962943e-02 3.271572e-03 1.962943e-02
#> 5019 1020.1 2018.1
#> 1.962943e-02 1.138507e-02 1.962943e-02
#> 2148.1 2153.3 2157.3
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 2176 2178 2179
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 2180 2181 2183
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2184 2190 2192
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 2193 2194 2195
#> 1.962943e-02 1.795071e-06 1.962943e-02
#> 2206 2220 4215
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4242 4251.1 4252.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4280 4297 4301.1
#> 1.877131e-04 1.877131e-04 1.877131e-04
#> 4318.1 4320.1 5410
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 5448.1 5449.1 5450
#> 1.962943e-02 1.673328e-04 1.962943e-02
#> 5451 5464 5467
#> 1.877131e-04 1.962943e-02 1.795071e-06
#> WA12-101402 WA9-111302 2027
#> 1.269976e-02 2.024096e-05 1.600177e-06
#> 1105 2222 2234.1
#> 1.962943e-02 1.962943e-02 3.271572e-03
#> 2234.2 2235.1 2235.2
#> 3.128552e-05 3.271572e-03 1.877131e-04
#> 2236 2236.10 2236.6
#> 1.877131e-04 1.962943e-02 1.962943e-02
#> 2236.7 2243.1 2243.3
#> 1.962943e-02 1.877131e-04 1.962943e-02
#> 2243.5 2243.6 2243.8
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2271 2274 2295
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2336.1 2336.2 2336.3
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2336.4 2336.5 2340
#> 1.962943e-02 1.962943e-02 1.795071e-06
#> 2344 2402 2404.1
#> 1.962943e-02 3.271572e-03 1.962943e-02
#> 2424 2542 2552
#> 1.962943e-02 1.620370e-03 1.962943e-02
#> 2554.4 2554.5 2572
#> 1.962943e-02 1.877131e-04 1.308629e-04
#> 2598 2611.1 2611.2
#> 1.877131e-04 1.962943e-02 1.962943e-02
#> 2611.3 2615 2617.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2617.2 2617.3 2622.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2622.2 2622.3 2624
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2628 2631 2634
#> 1.962943e-02 1.795071e-06 1.308629e-04
#> 2641.1 2641.2 2642
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2643 2644 2644.1
#> 1.877131e-04 1.962943e-02 1.962943e-02
#> 2644.2 2644.3 2647
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2647.1 2647.2 2648
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2649 2649.1 4239
#> 3.271572e-03 1.962943e-02 1.962943e-02
#> 4240 4347 4349
#> 1.962943e-02 1.795071e-06 1.673328e-04
#> 4351 4352 4353
#> 3.271572e-03 3.271572e-03 3.271572e-03
#> 4354 4355 4358
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4359 4361 4362
#> 1.877131e-04 1.877131e-04 1.962943e-02
#> 4364 4367 4375
#> 1.877131e-04 3.128552e-05 3.271572e-03
#> 4377 4378 4379
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4380 4382 4383
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4396 4400.1 WA12-030403
#> 1.877131e-04 3.128552e-05 1.269976e-02
#> WA12-1-101403 WA12-1-111003 WA12-112403
#> 1.269976e-02 1.269976e-02 1.269976e-02
#> WA12-2-031803 WA12-2-111003 WA12-3-091603
#> 1.269976e-02 1.269976e-02 1.269976e-02
#> WA12-3-111003 WA12-4-081803 WA15-1-031803
#> 1.269976e-02 1.269976e-02 1.161367e-06
#> WA15-3-080403 WA1-7-031803 WA4-4-031803
#> 5.474034e-03 2.116626e-03 1.269976e-02
#> WA9.1-030403 WA9-081803 = 1712 2234
#> 2.024096e-05 1.214458e-04 7.180284e-08
#> 2222.12 2294 2452
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2486 2561 2562
#> 1.962943e-02 7.851772e-04 7.851772e-04
#> 2595 2849 2850
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 2851 2965.2 2976
#> 1.962943e-02 1.877131e-04 1.962943e-02
#> 2985 2987 2988
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 4542 9004 9013
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 9022 9023 9032
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 9034 9038 WA1.2BA15-030104
#> 1.877131e-04 1.962943e-02 1.214458e-04
#> WA1-011304 WA1-032204 WA12-011304
#> 1.269976e-02 1.214458e-04 1.269976e-02
#> WA12-012604 WA12-040504 WA12-051704
#> 1.269976e-02 1.269976e-02 2.116626e-03
#> WA12-2-032204 WA16-011304 WA27-040504
#> 1.214458e-04 1.269976e-02 1.269976e-02
#> WA27-071904 WA9-020904 4384
#> 1.269976e-02 1.269976e-02 1.795071e-06
#> WA27-040205 9488 11075
#> 1.269976e-02 6.392045e-03 1.420455e-03
#> 10490.1 10490.2 10490.3
#> 1.041667e-02 1.041667e-02 1.041667e-02
#> 10490.4 10491.1 10491.2
#> 1.041667e-02 2.083333e-02 2.083333e-02
#> 10491.3 10492.1 10492.2
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 10492.3 10492.4 10492.5
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 10492.6 10493 10496.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 10496.2 10496.3 10497.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 10497.2 10497.3 11745.1
#> 6.313131e-04 2.083333e-02 2.083333e-02
#> 11745.2 11745.3 11761.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11761.2 11761.3 11761.4
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11761.5 11762.1 11762.2
#> 6.313131e-04 2.083333e-02 2.083333e-02
#> 11762.3 11803.1 11803.2
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11803.3 11805.1 11805.2
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11805.3 11806 11807.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11807.2 11807.3 11808.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11808.2 11808.3 11810.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11810.2 11810.3 11812.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11812.2 11812.3 11819.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11819.2 11819.3 11819.4
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11819.5 11819.6 11855.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11855.2 11913.1 11913.2
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11913.3 11914.1 11914.2
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11914.3 11349 11372
#> 2.083333e-02 7.520053e-04 1.671123e-04
#> 11798x7535 11799x7517 10794-V5
#> 1.041667e-02 2.083333e-02 3.240741e-04
#> 11466-V2 11466-V5 11540-V3
#> 8.847122e-05 8.847122e-05 3.240741e-03
#> 11160 11955 13150
#> 2.083333e-02 2.083333e-02 1.041667e-02
#> 13153.1 13153.2 13155
#> 4.861111e-03 4.861111e-03 2.083333e-02
#> 13184 13185 13205
#> 2.083333e-02 1.190476e-03 2.083333e-02
#> 13206 13207 13228
#> 2.083333e-02 1.041667e-02 1.041667e-02
#> 13154 11956 13226
#> 2.083333e-02 2.083333e-02 1.041667e-02
#> 13227 2043_1 2138_1
#> 1.041667e-02 1.962943e-02 1.962943e-02
#> 2157_3 11001 13592
#> 1.877131e-04 9.722222e-04 4.861111e-03
#> WA12S-091713 13746-9105 13766-9120
#> 1.673328e-04 4.166667e-03 1.877131e-04
#> 13767-9121 13773-9138 13774-9174
#> 1.877131e-04 1.962943e-02 1.041141e-06
#> 13778-9175 13780-9139 13781-9123
#> 3.128552e-05 1.962943e-02 1.673328e-04
#> 13782-9140 13785-9142 13786-9143
#> 1.962943e-02 4.629630e-04 4.629630e-04
#> 13787-9144 13788-9145 13789-9146
#> 4.629630e-04 2.558480e-04 4.861111e-03
#> 13790-9147 13835 13844-9176
#> 2.558480e-04 3.086420e-04 1.543210e-04
#> 13845-9124 13846-9108 13847-9109
#> 4.861111e-03 3.240741e-03 2.558480e-04
#> 13849-9110 13850-9111 13859-9112
#> 2.083333e-02 3.125000e-02 2.083333e-02
#> 13860-9148 13861-9113 13862-9114
#> 2.083333e-02 1.190476e-03 1.190476e-03
#> 13863-9115 13867-9117 13870-9149
#> 2.083333e-02 5.208333e-03 1.877131e-04
#> 13875-9132 13878-9151 13879-9152
#> 1.877131e-04 4.861111e-03 4.050926e-03
#> 13881-9153 13883-9133 13885-9177
#> 4.873294e-06 7.716049e-05 3.240741e-04
#> 13886-9154 13887-9202 13888
#> 1.620370e-03 3.240741e-04 5.692535e-03
#> 13889-9161 13891-9162 13893-9178
#> 3.271572e-03 9.722222e-04 2.430556e-03
#> 13895-9155 13900-9156 13902-9157
#> 4.861111e-03 4.861111e-03 7.520053e-04
#> 13903-9179 13904-9180 13905-9181
#> 1.138507e-02 1.410160e-03 7.520053e-04
#> 13906-9163 13908-9164 13909-9158
#> 7.520053e-04 7.520053e-04 1.877131e-04
#> 13916 13917-9182 13918-9203
#> 2.430556e-03 4.861111e-03 4.861111e-03
#> 13919-9183 13920-9159 13927-9185
#> 4.861111e-03 4.861111e-03 1.041667e-02
#> 13928-9186 13929-9187 13930-A-9188
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 13930-B 13932-9189 13933-9190
#> 2.083333e-02 4.861111e-03 1.620370e-03
#> 13934 13942-9194 13945
#> 7.812500e-03 1.388889e-04 3.086420e-04
#> 13951-9195 13952-9196 13954-9197
#> 1.785714e-03 2.083333e-02 1.190476e-03
#> 13955-9198 13957-9199 13958-9200
#> 1.190476e-03 2.083333e-02 1.785714e-03
#> 13959-9206 13960-9207 14001-9208
#> 3.125000e-02 3.125000e-02 3.240741e-03
#> 14002 14003-9209 14004
#> 4.861111e-03 2.916667e-03 9.722222e-04
#> 14005 14006-9210 14007-9211
#> 1.620370e-03 1.620370e-03 1.620370e-03
#> 14008-9212 14023 14024
#> 1.620370e-03 1.041667e-02 1.785714e-03
#> 14028 14033 14035
#> 2.083333e-02 9.259259e-05 3.086420e-04
#> 14036 14056 13872-9150
#> 9.259259e-05 2.916667e-03 1.962943e-02
#> 13893 13931-9204 13600
#> 4.861111e-03 2.430556e-03 3.271572e-03
#> 13632 13635 13655
#> 1.671123e-04 4.166667e-03 2.558480e-04
#> 13661 13662 13663
#> 4.861111e-03 3.240741e-03 1.535088e-04
#> 13690 13692 13694
#> 4.873294e-06 4.629630e-05 9.722222e-04
#> 13695 13698 13699
#> 5.116959e-05 6.481481e-04 4.861111e-03
#> 13711 13716 13735
#> 9.259259e-05 1.535088e-04 4.861111e-03
#> 13737 13738 13739
#> 1.620370e-03 3.240741e-03 3.240741e-03
#> 13744 13747 13748
#> 3.240741e-03 4.166667e-03 4.166667e-03
#> 13749 13751 13753
#> 2.083333e-03 4.166667e-03 4.166667e-03
#> H-2-040113 13801 13802
#> 1.671123e-04 5.116959e-05 1.620370e-03
#> 13805 13824 13825
#> 5.116959e-05 4.166667e-03 1.877131e-04
#> 13826 13827 13828
#> 1.795071e-06 1.877131e-04 4.166667e-03
#> 13830 13831 13832
#> 1.962943e-02 8.847122e-05 4.166667e-03
#> 13837 13838 13839
#> 4.166667e-03 4.166667e-03 4.166667e-03
#> 13840 13841 13842
#> 5.208333e-04 4.166667e-03 7.520053e-04
#> 2157-3 11001-8874 2027-1
#> 1.877131e-04 9.722222e-04 1.962943e-02
#> 2138-1 13873 14040
#> 1.962943e-02 1.877131e-04 4.873294e-06
#> 14041 14042 14043
#> 9.259259e-05 1.624431e-06 9.259259e-05
#> 14044 14046 14047
#> 1.543210e-04 4.861111e-03 7.520053e-04
#> 14049 14077 14078
#> 1.620370e-03 8.847122e-05 8.847122e-05
#> 14079 14080 14081
#> 8.847122e-05 8.847122e-05 8.847122e-05
#> 14082 14083 14085
#> 8.847122e-05 8.847122e-05 2.916667e-03
#> 14092 14093 14107
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 14108 14112 14113
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 14114 14115 14116
#> 2.558480e-04 3.240741e-03 2.314815e-04
#> 14119 14120 14121
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 14122 14123 14131
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 14132 14045-a 14045-b
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 13971 13977 14129
#> 7.520053e-04 1.620370e-03 1.420455e-03
#> 14135 14136 14137.1
#> 1.420455e-03 8.847122e-05 8.847122e-05
#> 14138 14139 14141
#> 2.893519e-03 8.847122e-05 4.861111e-03
#> 14142 14145 14149
#> 1.944444e-03 5.208333e-04 4.861111e-03
#> 14151 14152 14153
#> 7.520053e-04 7.520053e-04 7.520053e-04
#> 14156 14159 14160
#> 1.620370e-03 2.916667e-03 7.520053e-04
#> 14161 14162 14164
#> 1.877131e-04 7.520053e-04 6.392045e-03
#> 14165 14167 14168
#> 2.916667e-03 1.620370e-03 4.861111e-03
#> 14169 14171 14172
#> 2.558480e-04 4.861111e-03 1.279240e-04
#> 14174 14175 WA84-121613
#> 1.795071e-06 9.259259e-05 4.861111e-03
# You can also take the product of the non-logged results:
apply(pgen(Pram, log = FALSE), 1, prod, na.rm = TRUE)
#> 1411152-10B 82 83
#> 2.083333e-03 4.861111e-03 4.310345e-05
#> 84 85 81-NM-1
#> 2.011494e-04 9.722222e-03 4.861111e-03
#> 06-1413-1 07-83-7-A ODA-06-1029-82B
#> 4.185268e-03 4.715795e-04 4.185268e-03
#> ODA-06-1029-82C ODA-06-1029-109A ODA-06-1029-109B
#> 4.185268e-03 4.185268e-03 4.185268e-03
#> 118-28-A 08-206-44-B 08-206-44-D
#> 4.185268e-04 1.395089e-03 1.395089e-03
#> 08-206-44-E 351-5-A 351-5-C
#> 1.395089e-03 1.771191e-05 1.771191e-05
#> 351-5-D 351-5-E 04-76-C
#> 1.771191e-05 1.771191e-05 5.580357e-04
#> 04-335-2A 04-189-B4 03-74-N10A-B
#> 4.185268e-03 8.370536e-04 8.370536e-04
#> 05-2033-72 05-2033-73 05-2086-12
#> 4.715795e-04 4.715795e-04 1.395089e-03
#> 05-2086-20 05-2086-31 05-2086-34
#> 4.715795e-04 1.571932e-04 1.395089e-03
#> 05-2088-3 06-30 06-81-2
#> 4.185268e-03 4.185268e-03 1.395089e-03
#> 06-1036-71B 06-1036-71C 06-1029-122D
#> 4.185268e-03 4.185268e-03 4.185268e-03
#> 06-1029-122C 06-1029-122A 06-1029-98C
#> 4.185268e-04 4.185268e-04 1.771191e-05
#> 06-1027-90 1369017-9 1352535-6
#> 4.185268e-03 4.861111e-03 4.861111e-03
#> 1343990-17 1344272-8 1411152-10A
#> 1.005747e-04 4.861111e-03 2.083333e-03
#> 1341321-16 1418983-2 1402871-B
#> 4.161712e-06 1.041667e-03 2.011494e-04
#> 1373915-5 1343990-10 1360295-17
#> 2.011494e-04 4.861111e-03 2.011494e-04
#> 1341321-32 1339849-3 1339849-5
#> 2.011494e-04 4.861111e-03 4.861111e-03
#> 1339849-6 1339849-7 1339849-8
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 1339849-10 1339849-12 1339849-13
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 1339849-15 1339849-16 1339849-17
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 1429425 07-83-7-B 07-83-37-D
#> 4.861111e-03 1.395089e-03 4.185268e-03
#> 07-83-38-B 07-83-38-D 1370431-1
#> 4.185268e-03 4.185268e-04 9.722222e-03
#> 1370431-2 1370431-3 1370431-4
#> 9.722222e-03 2.011494e-04 2.011494e-04
#> 1370431-5 1428631-1 04-278-3
#> 9.722222e-03 1.005747e-04 4.185268e-03
#> 04-335-2B 04-335-2C 1314176-9
#> 4.185268e-03 3.143863e-05 4.861111e-03
#> 1314176-13 1387968 1418886
#> 4.861111e-03 1.005747e-04 2.011494e-04
#> 04-83D Phytr-06-4 Phytr-0-217
#> 5.580357e-04 2.430556e-03 4.861111e-03
#> NOR1.2 MCK1.1 MCK1.2
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 4123.100000000000364 07-1161-1C 07-1161-1E
#> 1.571932e-04 8.370536e-03 4.185268e-03
#> 07-1161-4A 07-1161-4B 07-1161-3-1
#> 4.185268e-03 1.395089e-03 4.185268e-03
#> 07-1161-3-2 07-1161-3-3 07-1161-5A
#> 4.185268e-03 4.185268e-03 1.395089e-03
#> 07-1161-5D 1314070-20 07-1240-1
#> 1.395089e-03 4.861111e-03 4.185268e-03
#> 08-15-1 08-16-1 1368791-19
#> 4.185268e-03 4.185268e-03 2.083333e-03
#> 1368791-21 1429891-1 1429891-2
#> 1.041667e-03 2.083333e-03 8.620690e-05
#> 1429891-3 1429891-4 1429891-6
#> 4.861111e-03 2.083333e-03 2.083333e-03
#> 1429891-7 1429891-10 1429891-11
#> 2.083333e-03 2.083333e-03 2.083333e-03
#> 1437044-28 1454471-29 1454471-31
#> 8.620690e-05 1.783591e-06 1.783591e-06
#> 1309326-1 1480397 1368791-2
#> 4.861111e-03 2.083333e-03 1.005747e-04
#> 1281744-1 1281744-3 1281744-5
#> 2.083333e-03 2.083333e-03 1.041667e-03
#> 1281744-6 1281744-7 1281744-9
#> 2.083333e-03 8.620690e-05 4.166667e-03
#> 1281744-10 1281744-15 1281744-16
#> 2.083333e-03 2.083333e-03 4.166667e-03
#> 1281744-21 1454527-12 1480844-4
#> 2.083333e-03 4.861111e-03 4.861111e-03
#> 1480844-5 1480844-8 1480844-10
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 1281744-4 1480841-6 1281789-1
#> 2.083333e-03 2.083333e-03 2.083333e-03
#> 1281789-2 1431833-31 1431833-32
#> 2.083333e-03 4.861111e-03 4.861111e-03
#> 1431833-39 1309305-21 118-28-B
#> 4.861111e-03 2.011494e-04 4.185268e-03
#> 118-28-E 134-19-E 134-20-E
#> 4.185268e-04 8.370536e-03 4.185268e-03
#> Pr 519- LTR1.2 Pr 520- MCK1.1 09-133-4 ODA
#> 9.722222e-03 4.861111e-03 1.395089e-03
#> SOD OR 10-59-3-A SOD OR 10-59-3-D SOD OR 10-59-3-E
#> 4.185268e-03 4.185268e-03 4.185268e-03
#> SOD OR 10-59-3-F SOD OR 10-59-3-H Pr 731
#> 4.185268e-03 4.185268e-03 5.208333e-04
#> Pr 732 Pr 733 Pr 734
#> 5.208333e-04 1.215278e-03 1.215278e-03
#> Pr 735 1441558-37 1441558-39
#> 1.215278e-03 4.861111e-03 9.722222e-03
#> 1469925-55 1538371-8 1560692-17
#> 1.783591e-06 9.722222e-03 1.340996e-04
#> 1623730-36 1623827-6 1631078-10
#> 9.722222e-03 9.722222e-03 4.861111e-03
#> 1631078-12 #4177 Blomquist back up 1631081-1
#> 9.722222e-03 4.861111e-03 4.861111e-03
#> 1631081-2 1631081-3 1631081-15
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 1631081-17 1631081-22 1644850-1
#> 9.722222e-03 4.861111e-03 9.722222e-03
#> 1644850-2 1644850-4 1644850-5
#> 9.722222e-03 9.722222e-03 9.722222e-03
#> 1644850-6 1644850-7 1644850-8
#> 9.722222e-03 4.861111e-03 9.722222e-03
#> 1644856-18 1644856-35 1341878-7
#> 9.722222e-03 9.722222e-03 8.620690e-05
#> 1341878-49 1365048 1496607
#> 2.083333e-03 2.011494e-04 2.011494e-04
#> 1560191-36 1583329-B 1583329-C
#> 4.161712e-06 2.011494e-04 4.861111e-03
#> 1596853 1596854 1621925-9
#> 9.722222e-03 8.620690e-05 9.722222e-03
#> 1621925-11 1621926-8 1626660-3
#> 9.722222e-03 9.722222e-03 9.722222e-03
#> 1625769 1626651-10 1626656-1
#> 2.011494e-04 9.722222e-03 9.722222e-03
#> 1644994-2 PC#11-1366 ODA 81-8
#> 9.722222e-03 4.861111e-03 1.771191e-05
#> ODA 81-9 ODA 81-37 ODA 114-6
#> 1.771191e-05 1.771191e-05 1.771191e-05
#> 120187 120189 120231
#> 3.143863e-05 4.861111e-03 2.011494e-04
#> 1404252-18 1497058-26 1644623-8
#> 2.011494e-04 8.620690e-05 2.011494e-04
#> 1644623-26 230P06005897-8 230P06005897-9
#> 4.161712e-06 2.011494e-04 2.011494e-04
#> 230P06005898-20 230P06005898-21 10998-V2
#> 2.011494e-04 2.011494e-04 1.571932e-05
#> 1004.1 1008.1 1019.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 1021.1 1030.1 1031.1
#> 3.128552e-05 1.962943e-02 1.962943e-02
#> 1032.1 1033.1 1041
#> 1.962943e-02 1.877131e-04 1.962943e-02
#> 1044 1055 2029.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2043.1 2091.1 2092
#> 1.962943e-02 1.962943e-02 1.673328e-04
#> 2096 2099.1 2108.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2108.2 2110.4 4088.1
#> 1.877131e-04 1.962943e-02 3.271572e-03
#> 4089.1 4120 4122.4
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4131 4143.1 4144.1
#> 1.962943e-02 3.271572e-03 1.962943e-02
#> 4146.1 4154 4158.2
#> 1.962943e-02 3.128552e-05 1.962943e-02
#> 4167.1 4168.2 4169.1
#> 1.877131e-04 1.877131e-04 1.962943e-02
#> 4172.2 4173.2 5013.1
#> 1.962943e-02 3.271572e-03 1.962943e-02
#> 5019 1020.1 2018.1
#> 1.962943e-02 1.138507e-02 1.962943e-02
#> 2148.1 2153.3 2157.3
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 2176 2178 2179
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 2180 2181 2183
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2184 2190 2192
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 2193 2194 2195
#> 1.962943e-02 1.795071e-06 1.962943e-02
#> 2206 2220 4215
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4242 4251.1 4252.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4280 4297 4301.1
#> 1.877131e-04 1.877131e-04 1.877131e-04
#> 4318.1 4320.1 5410
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 5448.1 5449.1 5450
#> 1.962943e-02 1.673328e-04 1.962943e-02
#> 5451 5464 5467
#> 1.877131e-04 1.962943e-02 1.795071e-06
#> WA12-101402 WA9-111302 2027
#> 1.269976e-02 2.024096e-05 1.600177e-06
#> 1105 2222 2234.1
#> 1.962943e-02 1.962943e-02 3.271572e-03
#> 2234.2 2235.1 2235.2
#> 3.128552e-05 3.271572e-03 1.877131e-04
#> 2236 2236.10 2236.6
#> 1.877131e-04 1.962943e-02 1.962943e-02
#> 2236.7 2243.1 2243.3
#> 1.962943e-02 1.877131e-04 1.962943e-02
#> 2243.5 2243.6 2243.8
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2271 2274 2295
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2336.1 2336.2 2336.3
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2336.4 2336.5 2340
#> 1.962943e-02 1.962943e-02 1.795071e-06
#> 2344 2402 2404.1
#> 1.962943e-02 3.271572e-03 1.962943e-02
#> 2424 2542 2552
#> 1.962943e-02 1.620370e-03 1.962943e-02
#> 2554.4 2554.5 2572
#> 1.962943e-02 1.877131e-04 1.308629e-04
#> 2598 2611.1 2611.2
#> 1.877131e-04 1.962943e-02 1.962943e-02
#> 2611.3 2615 2617.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2617.2 2617.3 2622.1
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2622.2 2622.3 2624
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2628 2631 2634
#> 1.962943e-02 1.795071e-06 1.308629e-04
#> 2641.1 2641.2 2642
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2643 2644 2644.1
#> 1.877131e-04 1.962943e-02 1.962943e-02
#> 2644.2 2644.3 2647
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2647.1 2647.2 2648
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2649 2649.1 4239
#> 3.271572e-03 1.962943e-02 1.962943e-02
#> 4240 4347 4349
#> 1.962943e-02 1.795071e-06 1.673328e-04
#> 4351 4352 4353
#> 3.271572e-03 3.271572e-03 3.271572e-03
#> 4354 4355 4358
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4359 4361 4362
#> 1.877131e-04 1.877131e-04 1.962943e-02
#> 4364 4367 4375
#> 1.877131e-04 3.128552e-05 3.271572e-03
#> 4377 4378 4379
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4380 4382 4383
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 4396 4400.1 WA12-030403
#> 1.877131e-04 3.128552e-05 1.269976e-02
#> WA12-1-101403 WA12-1-111003 WA12-112403
#> 1.269976e-02 1.269976e-02 1.269976e-02
#> WA12-2-031803 WA12-2-111003 WA12-3-091603
#> 1.269976e-02 1.269976e-02 1.269976e-02
#> WA12-3-111003 WA12-4-081803 WA15-1-031803
#> 1.269976e-02 1.269976e-02 1.161367e-06
#> WA15-3-080403 WA1-7-031803 WA4-4-031803
#> 5.474034e-03 2.116626e-03 1.269976e-02
#> WA9.1-030403 WA9-081803 = 1712 2234
#> 2.024096e-05 1.214458e-04 7.180284e-08
#> 2222.12 2294 2452
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 2486 2561 2562
#> 1.962943e-02 7.851772e-04 7.851772e-04
#> 2595 2849 2850
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 2851 2965.2 2976
#> 1.962943e-02 1.877131e-04 1.962943e-02
#> 2985 2987 2988
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 4542 9004 9013
#> 1.962943e-02 1.962943e-02 1.877131e-04
#> 9022 9023 9032
#> 1.962943e-02 1.962943e-02 1.962943e-02
#> 9034 9038 WA1.2BA15-030104
#> 1.877131e-04 1.962943e-02 1.214458e-04
#> WA1-011304 WA1-032204 WA12-011304
#> 1.269976e-02 1.214458e-04 1.269976e-02
#> WA12-012604 WA12-040504 WA12-051704
#> 1.269976e-02 1.269976e-02 2.116626e-03
#> WA12-2-032204 WA16-011304 WA27-040504
#> 1.214458e-04 1.269976e-02 1.269976e-02
#> WA27-071904 WA9-020904 4384
#> 1.269976e-02 1.269976e-02 1.795071e-06
#> WA27-040205 9488 11075
#> 1.269976e-02 6.392045e-03 1.420455e-03
#> 10490.1 10490.2 10490.3
#> 1.041667e-02 1.041667e-02 1.041667e-02
#> 10490.4 10491.1 10491.2
#> 1.041667e-02 2.083333e-02 2.083333e-02
#> 10491.3 10492.1 10492.2
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 10492.3 10492.4 10492.5
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 10492.6 10493 10496.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 10496.2 10496.3 10497.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 10497.2 10497.3 11745.1
#> 6.313131e-04 2.083333e-02 2.083333e-02
#> 11745.2 11745.3 11761.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11761.2 11761.3 11761.4
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11761.5 11762.1 11762.2
#> 6.313131e-04 2.083333e-02 2.083333e-02
#> 11762.3 11803.1 11803.2
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11803.3 11805.1 11805.2
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11805.3 11806 11807.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11807.2 11807.3 11808.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11808.2 11808.3 11810.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11810.2 11810.3 11812.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11812.2 11812.3 11819.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11819.2 11819.3 11819.4
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11819.5 11819.6 11855.1
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11855.2 11913.1 11913.2
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11913.3 11914.1 11914.2
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 11914.3 11349 11372
#> 2.083333e-02 7.520053e-04 1.671123e-04
#> 11798x7535 11799x7517 10794-V5
#> 1.041667e-02 2.083333e-02 3.240741e-04
#> 11466-V2 11466-V5 11540-V3
#> 8.847122e-05 8.847122e-05 3.240741e-03
#> 11160 11955 13150
#> 2.083333e-02 2.083333e-02 1.041667e-02
#> 13153.1 13153.2 13155
#> 4.861111e-03 4.861111e-03 2.083333e-02
#> 13184 13185 13205
#> 2.083333e-02 1.190476e-03 2.083333e-02
#> 13206 13207 13228
#> 2.083333e-02 1.041667e-02 1.041667e-02
#> 13154 11956 13226
#> 2.083333e-02 2.083333e-02 1.041667e-02
#> 13227 2043_1 2138_1
#> 1.041667e-02 1.962943e-02 1.962943e-02
#> 2157_3 11001 13592
#> 1.877131e-04 9.722222e-04 4.861111e-03
#> WA12S-091713 13746-9105 13766-9120
#> 1.673328e-04 4.166667e-03 1.877131e-04
#> 13767-9121 13773-9138 13774-9174
#> 1.877131e-04 1.962943e-02 1.041141e-06
#> 13778-9175 13780-9139 13781-9123
#> 3.128552e-05 1.962943e-02 1.673328e-04
#> 13782-9140 13785-9142 13786-9143
#> 1.962943e-02 4.629630e-04 4.629630e-04
#> 13787-9144 13788-9145 13789-9146
#> 4.629630e-04 2.558480e-04 4.861111e-03
#> 13790-9147 13835 13844-9176
#> 2.558480e-04 3.086420e-04 1.543210e-04
#> 13845-9124 13846-9108 13847-9109
#> 4.861111e-03 3.240741e-03 2.558480e-04
#> 13849-9110 13850-9111 13859-9112
#> 2.083333e-02 3.125000e-02 2.083333e-02
#> 13860-9148 13861-9113 13862-9114
#> 2.083333e-02 1.190476e-03 1.190476e-03
#> 13863-9115 13867-9117 13870-9149
#> 2.083333e-02 5.208333e-03 1.877131e-04
#> 13875-9132 13878-9151 13879-9152
#> 1.877131e-04 4.861111e-03 4.050926e-03
#> 13881-9153 13883-9133 13885-9177
#> 4.873294e-06 7.716049e-05 3.240741e-04
#> 13886-9154 13887-9202 13888
#> 1.620370e-03 3.240741e-04 5.692535e-03
#> 13889-9161 13891-9162 13893-9178
#> 3.271572e-03 9.722222e-04 2.430556e-03
#> 13895-9155 13900-9156 13902-9157
#> 4.861111e-03 4.861111e-03 7.520053e-04
#> 13903-9179 13904-9180 13905-9181
#> 1.138507e-02 1.410160e-03 7.520053e-04
#> 13906-9163 13908-9164 13909-9158
#> 7.520053e-04 7.520053e-04 1.877131e-04
#> 13916 13917-9182 13918-9203
#> 2.430556e-03 4.861111e-03 4.861111e-03
#> 13919-9183 13920-9159 13927-9185
#> 4.861111e-03 4.861111e-03 1.041667e-02
#> 13928-9186 13929-9187 13930-A-9188
#> 2.083333e-02 2.083333e-02 2.083333e-02
#> 13930-B 13932-9189 13933-9190
#> 2.083333e-02 4.861111e-03 1.620370e-03
#> 13934 13942-9194 13945
#> 7.812500e-03 1.388889e-04 3.086420e-04
#> 13951-9195 13952-9196 13954-9197
#> 1.785714e-03 2.083333e-02 1.190476e-03
#> 13955-9198 13957-9199 13958-9200
#> 1.190476e-03 2.083333e-02 1.785714e-03
#> 13959-9206 13960-9207 14001-9208
#> 3.125000e-02 3.125000e-02 3.240741e-03
#> 14002 14003-9209 14004
#> 4.861111e-03 2.916667e-03 9.722222e-04
#> 14005 14006-9210 14007-9211
#> 1.620370e-03 1.620370e-03 1.620370e-03
#> 14008-9212 14023 14024
#> 1.620370e-03 1.041667e-02 1.785714e-03
#> 14028 14033 14035
#> 2.083333e-02 9.259259e-05 3.086420e-04
#> 14036 14056 13872-9150
#> 9.259259e-05 2.916667e-03 1.962943e-02
#> 13893 13931-9204 13600
#> 4.861111e-03 2.430556e-03 3.271572e-03
#> 13632 13635 13655
#> 1.671123e-04 4.166667e-03 2.558480e-04
#> 13661 13662 13663
#> 4.861111e-03 3.240741e-03 1.535088e-04
#> 13690 13692 13694
#> 4.873294e-06 4.629630e-05 9.722222e-04
#> 13695 13698 13699
#> 5.116959e-05 6.481481e-04 4.861111e-03
#> 13711 13716 13735
#> 9.259259e-05 1.535088e-04 4.861111e-03
#> 13737 13738 13739
#> 1.620370e-03 3.240741e-03 3.240741e-03
#> 13744 13747 13748
#> 3.240741e-03 4.166667e-03 4.166667e-03
#> 13749 13751 13753
#> 2.083333e-03 4.166667e-03 4.166667e-03
#> H-2-040113 13801 13802
#> 1.671123e-04 5.116959e-05 1.620370e-03
#> 13805 13824 13825
#> 5.116959e-05 4.166667e-03 1.877131e-04
#> 13826 13827 13828
#> 1.795071e-06 1.877131e-04 4.166667e-03
#> 13830 13831 13832
#> 1.962943e-02 8.847122e-05 4.166667e-03
#> 13837 13838 13839
#> 4.166667e-03 4.166667e-03 4.166667e-03
#> 13840 13841 13842
#> 5.208333e-04 4.166667e-03 7.520053e-04
#> 2157-3 11001-8874 2027-1
#> 1.877131e-04 9.722222e-04 1.962943e-02
#> 2138-1 13873 14040
#> 1.962943e-02 1.877131e-04 4.873294e-06
#> 14041 14042 14043
#> 9.259259e-05 1.624431e-06 9.259259e-05
#> 14044 14046 14047
#> 1.543210e-04 4.861111e-03 7.520053e-04
#> 14049 14077 14078
#> 1.620370e-03 8.847122e-05 8.847122e-05
#> 14079 14080 14081
#> 8.847122e-05 8.847122e-05 8.847122e-05
#> 14082 14083 14085
#> 8.847122e-05 8.847122e-05 2.916667e-03
#> 14092 14093 14107
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 14108 14112 14113
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 14114 14115 14116
#> 2.558480e-04 3.240741e-03 2.314815e-04
#> 14119 14120 14121
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 14122 14123 14131
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 14132 14045-a 14045-b
#> 4.861111e-03 4.861111e-03 4.861111e-03
#> 13971 13977 14129
#> 7.520053e-04 1.620370e-03 1.420455e-03
#> 14135 14136 14137.1
#> 1.420455e-03 8.847122e-05 8.847122e-05
#> 14138 14139 14141
#> 2.893519e-03 8.847122e-05 4.861111e-03
#> 14142 14145 14149
#> 1.944444e-03 5.208333e-04 4.861111e-03
#> 14151 14152 14153
#> 7.520053e-04 7.520053e-04 7.520053e-04
#> 14156 14159 14160
#> 1.620370e-03 2.916667e-03 7.520053e-04
#> 14161 14162 14164
#> 1.877131e-04 7.520053e-04 6.392045e-03
#> 14165 14167 14168
#> 2.916667e-03 1.620370e-03 4.861111e-03
#> 14169 14171 14172
#> 2.558480e-04 4.861111e-03 1.279240e-04
#> 14174 14175 WA84-121613
#> 1.795071e-06 9.259259e-05 4.861111e-03
## Rare Allele Correction ---------------------------------------------------
##
# If you don't supply a table of frequencies, they are calculated with rraf
# with correction = TRUE. This is normally benign when analyzing large
# populations, but it can have a great effect on small populations. To help
# control this, you can supply arguments described in
# help("rare_allele_correction").
# Default is to correct by 1/n per population. Since the calculation is
# performed on a smaller sample size due to round robin clone correction, it
# would be more appropriate to correct by 1/rrmlg at each locus. This is
# acheived by setting d = "rrmlg". Since this is a diploid, we would want to
# account for the number of chromosomes, and so we set mul = 1/2
head(pgen(Pram, log = FALSE, d = "rrmlg", mul = 1/2)) # compare with the output above
#> PrMS6A1 Pr9C3A1 PrMS39A1 PrMS45A1 PrMS43A1
#> 1411152-10B 0.5 0.5 0.15 0.5 0.11111111
#> 82 0.5 0.5 0.35 0.5 0.11111111
#> 83 0.5 0.5 0.15 0.5 0.05555556
#> 84 0.5 0.5 0.35 0.5 0.11111111
#> 85 0.5 0.5 0.35 0.5 0.22222222
#> 81-NM-1 0.5 0.5 0.35 0.5 0.11111111
# If you wanted to treat all alleles as equally rare, then you would set a
# specific value (let's say the rare alleles are 1/100):
head(pgen(Pram, log = FALSE, e = 1/100))
#> PrMS6A1 Pr9C3A1 PrMS39A1 PrMS45A1 PrMS43A1
#> 1411152-10B 0.5 0.5 0.15 0.5 0.111111111
#> 82 0.5 0.5 0.35 0.5 0.111111111
#> 83 0.5 0.5 0.15 0.5 0.003333333
#> 84 0.5 0.5 0.35 0.5 0.006666667
#> 85 0.5 0.5 0.35 0.5 0.222222222
#> 81-NM-1 0.5 0.5 0.35 0.5 0.111111111
# }