Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold

Calculates the observed heterozygosity for each individual in a genlight object and filters individuals based on specified threshold values. Use gl.report.heterozygosity to determine the appropriate thresholds.

Usage

gl.filter.heterozygosity(x, t.upper = 0.7, t.lower = 0, verbose = NULL)

Arguments

x

A genlight object containing the SNP genotypes [required].

t.upper

Filter individuals > the threshold [default 0.7].

t.lower

Filter individuals < the threshold [default 0].

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Value

The filtered genlight object.

See also

Other filter functions: gl.filter.allna(), gl.filter.callrate(), gl.filter.hwe(), gl.filter.ld(), gl.filter.locmetric(), gl.filter.maf(), gl.filter.monomorphs(), gl.filter.overshoot(), gl.filter.pa(), gl.filter.parent.offspring(), gl.filter.rdepth(), gl.filter.reproducibility(), gl.filter.secondaries(), gl.filter.sexlinked(), gl.filter.taglength()

Author

Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr

Examples

 result <- gl.filter.heterozygosity(testset.gl,t.upper=0.06,verbose=3)
#> Starting gl.filter.heterozygosity 
#>   Processing genlight object with SNP data
#>   Warning: genlight object contains monomorphic loci which will
#>                 be factored into heterozygosity estimates
#>   Retaining individuals with heterozygosity in the range 0 to 0.06 
#>   Minimum individual heterozygosity 0 
#>   Maximum individual heterozygosity 0.0866 
#>   Initial number of individuals: 250 
#>   Number of outlier individuals (heterozygosity  > 0.06 ): 1 
#>     Deleted: AA019157[EmmacRussEube],  Number of individuals retained: 249 
#> Completed: gl.filter.heterozygosity 
#> 
 tmp <- gl.report.heterozygosity(result,method='ind')
#> Starting gl.report.heterozygosity 
#>   Processing genlight object with SNP data
#>   Calculating observed heterozygosity for individuals
#>   Note: No adjustment for invariant loci (n.invariant set to 0)
#> 

#>   ind.name          Ho f.hom.ref f.hom.alt
#>   AA010915 0.009174312 0.6880734 0.3027523
#>   UC_00126 0.008695652 0.6608696 0.3304348
#>   AA032760 0.004926108 0.6699507 0.3251232
#>   AA013214 0.000000000 0.6525424 0.3474576
#>   AA011723 0.009049774 0.6651584 0.3257919
#>   AA012411 0.000000000 0.6682028 0.3317972
#>   AA019237 0.004504505 0.6801802 0.3153153
#>   AA019238 0.008849558 0.6769912 0.3141593
#>   AA019239 0.009132420 0.6712329 0.3196347
#>   AA019235 0.000000000 0.6801802 0.3198198
#>   AA019240 0.000000000 0.6740088 0.3259912
#>   AA019241 0.008810573 0.6607930 0.3303965
#>   AA019242 0.000000000 0.6724138 0.3275862
#>   AA019243 0.004385965 0.6710526 0.3245614
#>   AA019251 0.008968610 0.6591928 0.3318386
#>   AA019252 0.004545455 0.6727273 0.3227273
#>   AA012405 0.004524887 0.6606335 0.3348416
#>   AA012406 0.004504505 0.6531532 0.3423423
#>   AA012409 0.000000000 0.6607930 0.3392070
#>   AA012499 0.004484305 0.6681614 0.3273543
#>   AA012422 0.004566210 0.6712329 0.3242009
#>   AA012434 0.008928571 0.6607143 0.3303571
#>   AA012469 0.009009009 0.6486486 0.3423423
#>   AA012500 0.004524887 0.6651584 0.3303167
#>   AA032799 0.004329004 0.6580087 0.3376623
#>   AA032826 0.000000000 0.6830357 0.3169643
#>   AA010795 0.004629630 0.6898148 0.3055556
#>   AA010796 0.008620690 0.6551724 0.3362069
#>   AA032800 0.008810573 0.6651982 0.3259912
#>   AA032801 0.008733624 0.6637555 0.3275109
#>   AA032808 0.000000000 0.6846847 0.3153153
#>   AA032809 0.004405286 0.6784141 0.3171806
#>   AA032811 0.004484305 0.6681614 0.3273543
#>   AA032812 0.000000000 0.6801802 0.3198198
#>   AA032822 0.004424779 0.6681416 0.3274336
#>   AA032825 0.004405286 0.6607930 0.3348018
#>   AA010797 0.008888889 0.6755556 0.3155556
#>   AA010752 0.004424779 0.6769912 0.3185841
#>   AA010754 0.004405286 0.6740088 0.3215859
#>   AA010756 0.009132420 0.6757991 0.3150685
#>   AA010798 0.004444444 0.6755556 0.3200000
#>   AA010799 0.004310345 0.6465517 0.3491379
#>   AA010800 0.004424779 0.6858407 0.3097345
#>   AA010802 0.004405286 0.6651982 0.3303965
#>   AA010803 0.004424779 0.6769912 0.3185841
#>   AA010804 0.004651163 0.6837209 0.3116279
#>   AA010809 0.004424779 0.6637168 0.3318584
#>   AA010749 0.004385965 0.6622807 0.3333333
#>   AA010758 0.004255319 0.6553191 0.3404255
#>   AA010763 0.004385965 0.6622807 0.3333333
#>   AA010765 0.008583691 0.6609442 0.3304721
#>   AA010771 0.004484305 0.6681614 0.3273543
#>   AA010772 0.004524887 0.6787330 0.3167421
#>   AA010781 0.008928571 0.6696429 0.3214286
#>   AA032762 0.004424779 0.6681416 0.3274336
#>   AA032763 0.004484305 0.6771300 0.3183857
#>   AA032756 0.013274336 0.6592920 0.3274336
#>   AA032757 0.004524887 0.6923077 0.3031674
#>   AA032758 0.008928571 0.6651786 0.3258929
#>   AA032761 0.000000000 0.6772727 0.3227273
#>   AA032765 0.004366812 0.6681223 0.3275109
#>   AA010931 0.004405286 0.6740088 0.3215859
#>   AA010937 0.004385965 0.6622807 0.3333333
#>   AA010940 0.000000000 0.6637168 0.3362832
#>   AA032764 0.008403361 0.6470588 0.3445378
#>   AA032768 0.008810573 0.6607930 0.3303965
#>   AA010936 0.000000000 0.6846847 0.3153153
#>   AA010909 0.008928571 0.6741071 0.3169643
#>   AA010916 0.000000000 0.6787330 0.3212670
#>   AA010917 0.004484305 0.6771300 0.3183857
#>   AA010920 0.004385965 0.6710526 0.3245614
#>   AA010921 0.004524887 0.6651584 0.3303167
#>   AA020651 0.004385965 0.6710526 0.3245614
#>   AA020652 0.004484305 0.6636771 0.3318386
#>   AA020667 0.000000000 0.6637931 0.3362069
#>   AA020669 0.000000000 0.6666667 0.3333333
#>   AA020655 0.004385965 0.6666667 0.3289474
#>   AA020656 0.009009009 0.6846847 0.3063063
#>   AA020644 0.008810573 0.6740088 0.3171806
#>   AA020645 0.000000000 0.6651982 0.3348018
#>   AA020646 0.004366812 0.6593886 0.3362445
#>   AA020649 0.004484305 0.6771300 0.3183857
#>   AA013203 0.009049774 0.6696833 0.3212670
#>   AA013217 0.004464286 0.6741071 0.3214286
#>   AA013220 0.000000000 0.6637555 0.3362445
#>   AA013202 0.008888889 0.6755556 0.3155556
#>   AA013225 0.004347826 0.6782609 0.3173913
#>   AA018496 0.008888889 0.6800000 0.3111111
#>   AA018497 0.013452915 0.6816143 0.3049327
#>   AA018513 0.013636364 0.6590909 0.3272727
#>   AA013231 0.000000000 0.6681223 0.3318777
#>   AA013261 0.004385965 0.6578947 0.3377193
#>   AA013265 0.000000000 0.6724138 0.3275862
#>   AA013270 0.004566210 0.6849315 0.3105023
#>   AA018492 0.008888889 0.6711111 0.3200000
#>   AA018493 0.013574661 0.6742081 0.3122172
#>   AA018494 0.004761905 0.6809524 0.3142857
#>   AA018495 0.004524887 0.6787330 0.3167421
#>   AA018514 0.008658009 0.6580087 0.3333333
#>   AA018515 0.008620690 0.6637931 0.3275862
#>   AA018516 0.008888889 0.6711111 0.3200000
#>   UC_00125 0.000000000 0.6863636 0.3136364
#>  UC_00126a 0.009132420 0.6712329 0.3196347
#>   UC_00146 0.000000000 0.6976744 0.3023256
#>   UC_00149 0.004464286 0.6696429 0.3258929
#>   AA018640 0.017777778 0.6622222 0.3200000
#>   AA018658 0.000000000 0.6757991 0.3242009
#>   AA011729 0.018181818 0.6727273 0.3090909
#>   UC_00132 0.000000000 0.6636364 0.3363636
#>   UC_00137 0.008547009 0.6581197 0.3333333
#>   UC_00143 0.004587156 0.6743119 0.3211009
#>   UC_00157 0.004464286 0.6651786 0.3303571
#>   UC_00161 0.004504505 0.6801802 0.3153153
#>   AA018637 0.004672897 0.6869159 0.3084112
#>   AA018638 0.000000000 0.6863636 0.3136364
#>   AA018639 0.000000000 0.6697248 0.3302752
#>   AA011731 0.008474576 0.6483051 0.3432203
#>   AA033576 0.008771930 0.6622807 0.3289474
#>   AA033577 0.008888889 0.6711111 0.3200000
#>   AA011732 0.013157895 0.6622807 0.3245614
#>   AA011737 0.030434783 0.6478261 0.3217391
#>   AA011741 0.013157895 0.6535088 0.3333333
#>   AA011744 0.000000000 0.6784141 0.3215859
#>   AA011745 0.013392857 0.6651786 0.3214286
#>   AA011746 0.017699115 0.6637168 0.3185841
#>   AA011749 0.013274336 0.6504425 0.3362832
#>   AA033575 0.004464286 0.6741071 0.3214286
#>   AA033578 0.004347826 0.6608696 0.3347826
#>  AA012411a 0.000000000 0.6726457 0.3273543
#>   AA033579 0.004484305 0.6547085 0.3408072
#>   AA033582 0.008888889 0.6622222 0.3288889
#>   AA033593 0.004504505 0.6756757 0.3198198
#>   AA033602 0.000000000 0.6623377 0.3376623
#>   AA033609 0.004444444 0.6666667 0.3288889
#>   AA033617 0.009049774 0.6696833 0.3212670
#>  AA010915a 0.004524887 0.6832579 0.3122172
#>  AA011723a 0.009132420 0.6757991 0.3150685
#>   AA019158 0.000000000 0.6801802 0.3198198
#>   AA020379 0.004524887 0.6696833 0.3257919
#>   UC_01044 0.000000000 0.6785714 0.3214286
#>   AA018380 0.008733624 0.6593886 0.3318777
#>   AA018371 0.004366812 0.6550218 0.3406114
#>   AA004553 0.008810573 0.6651982 0.3259912
#>   AA000328 0.004484305 0.6681614 0.3273543
#>   AA000311 0.004566210 0.6621005 0.3333333
#>   AA019159 0.000000000 0.6901408 0.3098592
#>   AA020378 0.009049774 0.6651584 0.3257919
#>   UC_01060 0.004484305 0.6726457 0.3228700
#>   AA018379 0.009216590 0.6820276 0.3087558
#>   AA018365 0.004464286 0.6785714 0.3169643
#>   AA004554 0.022026432 0.6519824 0.3259912
#>   AA000303 0.004385965 0.6666667 0.3289474
#>   AA000320 0.009090909 0.6636364 0.3272727
#>   AA019160 0.004587156 0.6743119 0.3211009
#>   AA020377 0.008849558 0.6681416 0.3230088
#>   UC_01053 0.000000000 0.6637555 0.3362445
#>   AA018375 0.009090909 0.6545455 0.3363636
#>   AA004555 0.017777778 0.6533333 0.3288889
#>   AA000304 0.004484305 0.6681614 0.3273543
#>   AA019165 0.004629630 0.6759259 0.3194444
#>   AA019161 0.000000000 0.6772727 0.3227273
#>   AA020376 0.008968610 0.6771300 0.3139013
#>   UC_01062 0.004385965 0.6622807 0.3333333
#>   AA018374 0.013574661 0.6651584 0.3212670
#>    AA04523 0.026666667 0.6577778 0.3155556
#>   AA000305 0.004484305 0.6726457 0.3228700
#>   AA019164 0.000000000 0.6729858 0.3270142
#>   AA020375 0.004566210 0.6666667 0.3287671
#>   AA018373 0.018099548 0.6515837 0.3303167
#>   AA032875 0.021834061 0.6550218 0.3231441
#>   AA000309 0.000000000 0.6500000 0.3500000
#>   AA019163 0.004504505 0.6756757 0.3198198
#>   AA020374 0.008888889 0.6400000 0.3511111
#>   AA018368 0.008849558 0.6592920 0.3318584
#>   AA032878 0.013333333 0.6622222 0.3244444
#>   AA000302 0.013636364 0.6681818 0.3181818
#>   AA019162 0.004504505 0.6666667 0.3288288
#>   AA020365 0.000000000 0.6621622 0.3378378
#>   UC_00150 0.008695652 0.6652174 0.3260870
#>   AA018369 0.022222222 0.6577778 0.3200000
#>   AA004551 0.009049774 0.6606335 0.3303167
#>   AA032880 0.026315789 0.6578947 0.3157895
#>   AA000307 0.009009009 0.6666667 0.3243243
#>   AA019156 0.004524887 0.6696833 0.3257919
#>   AA020371 0.004424779 0.6548673 0.3407080
#>   UC_01051 0.004385965 0.6710526 0.3245614
#>   AA018370 0.004444444 0.6577778 0.3377778
#>   AA004552 0.021929825 0.6491228 0.3289474
#>   AA032882 0.004444444 0.6800000 0.3155556
#>   AA000310 0.013513514 0.6621622 0.3243243
#>   AA019075 0.004347826 0.6565217 0.3391304
#>   AA004864 0.008733624 0.6550218 0.3362445
#>   AA019071 0.008583691 0.6652361 0.3261803
#>   AA004868 0.000000000 0.6580087 0.3419913
#>   AA019083 0.000000000 0.6725664 0.3274336
#>   AA019072 0.008810573 0.6607930 0.3303965
#>   AA004858 0.008733624 0.6593886 0.3318777
#>   AA004869 0.017391304 0.6521739 0.3304348
#>   AA019082 0.013100437 0.6462882 0.3406114
#>   AA019073 0.000000000 0.6531532 0.3468468
#>   AA004859 0.013100437 0.6550218 0.3318777
#>   AA004866 0.004444444 0.6844444 0.3111111
#>   AA019077 0.008888889 0.6755556 0.3155556
#>   AA004860 0.008695652 0.6652174 0.3260870
#>   AA019080 0.000000000 0.6710526 0.3289474
#>   AA004861 0.000000000 0.6666667 0.3333333
#>   AA019079 0.004347826 0.6695652 0.3260870
#>   AA004862 0.012987013 0.6580087 0.3290043
#>   AA019078 0.004405286 0.6696035 0.3259912
#>   AA004863 0.013100437 0.6637555 0.3231441
#>   UC_00267 0.013824885 0.6405530 0.3456221
#>   UC_00205 0.036529680 0.6301370 0.3333333
#>   UC_00206 0.033333333 0.6523810 0.3142857
#>   UC_00208 0.018691589 0.6401869 0.3411215
#>   UC_00243 0.018604651 0.6279070 0.3534884
#>   UC_00209 0.009433962 0.6650943 0.3254717
#>   UC_00254 0.014150943 0.6367925 0.3490566
#>   UC_00210 0.023923445 0.6459330 0.3301435
#>   UC_00259 0.014354067 0.6507177 0.3349282
#>  UC_00126c 0.009389671 0.6384977 0.3521127
#>   AA063718 0.015151515 0.6919192 0.2929293
#>   AA063720 0.010204082 0.7142857 0.2755102
#>   AA063722 0.005235602 0.6963351 0.2984293
#>   AA063726 0.020942408 0.6910995 0.2879581
#>   AA063732 0.010256410 0.6923077 0.2974359
#>   AA063708 0.010152284 0.6903553 0.2994924
#>   AA063710 0.010101010 0.6969697 0.2929293
#>   AA063712 0.000000000 0.7040816 0.2959184
#>   AA063714 0.000000000 0.7020202 0.2979798
#>   AA063716 0.005025126 0.6934673 0.3015075
#>   AA020735 0.000000000 0.6593886 0.3406114
#>   AA032442 0.000000000 0.6623377 0.3376623
#>   AA032441 0.008658009 0.6536797 0.3376623
#>   AA020749 0.004273504 0.6495726 0.3461538
#>   AA020746 0.004310345 0.6681034 0.3275862
#>   AA020744 0.008695652 0.6565217 0.3347826
#>   AA020743 0.000000000 0.6709402 0.3290598
#>   AA020739 0.008771930 0.6666667 0.3245614
#>   AA020738 0.000000000 0.6710526 0.3289474
#>   AA001451 0.004291845 0.6480687 0.3476395
#>    AA01452 0.012875536 0.6523605 0.3347639
#>   AA001454 0.008695652 0.6434783 0.3478261
#>   AA001455 0.004255319 0.6468085 0.3489362
#>   AA001446 0.000000000 0.6536797 0.3463203
#>   AA001456 0.004310345 0.6465517 0.3491379
#>   AA001447 0.000000000 0.6523605 0.3476395
#>   AA001448 0.000000000 0.6465517 0.3534483
#>   AA001449 0.008620690 0.6422414 0.3491379
#>   AA001450 0.008510638 0.6468085 0.3446809
#> Completed: gl.report.heterozygosity 
#>