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test.R
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head(cd)
MarkerName Allele1 Allele2 Freq1 FreqSE MinFreq MaxFreq Effect
1 chr1:108391:A:G a g 0.0021 0 0.0021 0.0021 -0.4717
2 chr1:115637:G:A g a 0.0024 0 0.0024 0.0024 0.0883
3 chr1:137928:G:A g a 0.0008 0 0.0008 0.0008 1.2618
4 chr1:181729:CGGTGCT:C cggtgct c 0.0016 0 0.0016 0.0016 -0.4731
5 chr1:184280:C:T c t 0.0016 0 0.0016 0.0016 -0.4530
6 chr1:502543:G:C g c 0.0023 0 0.0023 0.0023 -0.1464
StdErr P.value Direction HetISq HetChiSq HetDf HetPVal CHR BP AF_EAS
1 0.5444 0.3862 ?????- 0 0 0 1 1 108391 NA
2 0.4823 0.8548 ?????+ 0 0 0 1 1 115637 NA
3 0.8752 0.1494 ?????+ 0 0 0 1 1 137928 NA
4 0.5306 0.3726 -????? 0 0 0 1 1 181729 0.0016
5 0.6109 0.4584 ?????- 0 0 0 1 1 184280 NA
6 0.4896 0.7649 ?????- 0 0 0 1 1 502543 NA
BETA_EAS SE_EAS P_EAS AF_NFE BETA_NFE SE_NFE P_NFE AF_FIN BETA_FIN
1 NA NA NA NA NA NA NA 0.002050390 -0.471690
2 NA NA NA NA NA NA NA 0.002424330 0.088258
3 NA NA NA NA NA NA NA 0.000840116 1.261770
4 -0.4731 0.5306 0.3726 NA NA NA NA NA NA
5 NA NA NA NA NA NA NA 0.001622210 -0.452999
6 NA NA NA NA NA NA NA 0.002333860 -0.146399
SE_FIN P_FIN
1 0.544360 0.386214
2 0.482285 0.854798
3 0.875245 0.149409
4 NA NA
5 0.610914 0.458384
6 0.489591 0.764923
str(cd)
MarkerName Allele1 Allele2 Freq1
Length:23077455 Length:23077455 Length:23077455 Min. :0.0000
Class :character Class :character Class :character 1st Qu.:0.0023
Mode :character Mode :character Mode :character Median :0.0124
Mean :0.1203
3rd Qu.:0.1352
Max. :1.0000
FreqSE MinFreq MaxFreq Effect
Min. :0.00000 Min. :0.00000 Min. :0.0000 Min. :-69.59230
1st Qu.:0.00000 1st Qu.:0.00170 1st Qu.:0.0023 1st Qu.: -0.07580
Median :0.00090 Median :0.00690 Median :0.0140 Median : -0.00140
Mean :0.01727 Mean :0.09083 Mean :0.1437 Mean : -0.00969
3rd Qu.:0.01660 3rd Qu.:0.06010 3rd Qu.:0.1681 3rd Qu.: 0.06020
Max. :0.44790 Max. :1.00000 Max. :1.0000 Max. : 47.20620
StdErr P.value Direction HetISq
Min. : 0.0123 Min. :0.0000 Length:23077455 Min. : 0.000
1st Qu.: 0.0290 1st Qu.:0.2328 Class :character 1st Qu.: 0.000
Median : 0.1241 Median :0.4779 Mode :character Median : 0.000
Mean : 0.2784 Mean :0.4847 Mean : 8.577
3rd Qu.: 0.4267 3rd Qu.:0.7356 3rd Qu.: 0.000
Max. :125.5900 Max. :1.0000 Max. :98.700
HetChiSq HetDf HetPVal CHR
Min. : 0.000 Min. :0.000 Min. :0.0000 Length:23077455
1st Qu.: 0.000 1st Qu.:0.000 1st Qu.:0.4245 Class :character
Median : 0.152 Median :1.000 Median :0.8671 Mode :character
Mean : 1.492 Mean :1.419 Mean :0.7087
3rd Qu.: 2.101 3rd Qu.:3.000 3rd Qu.:1.0000
Max. :376.200 Max. :5.000 Max. :1.0000
BP AF_EAS BETA_EAS SE_EAS
Min. : 10180 Min. :0 Min. :-312 Min. : 0
1st Qu.: 33227117 1st Qu.:0 1st Qu.: 0 1st Qu.: 0
Median : 69829944 Median :0 Median : 0 Median : 0
Mean : 78781505 Mean :0 Mean : 0 Mean : 0
3rd Qu.:114061994 3rd Qu.:0 3rd Qu.: 0 3rd Qu.: 0
Max. :248945195 Max. :1 Max. : 48 Max. :302
NA's :9579373 NA's :9579373 NA's :9579373
P_EAS AF_NFE BETA_NFE SE_NFE
Min. :0 Min. :0 Min. :-1 Min. :0
1st Qu.:0 1st Qu.:0 1st Qu.: 0 1st Qu.:0
Median :0 Median :0 Median : 0 Median :0
Mean :0 Mean :0 Mean : 0 Mean :0
3rd Qu.:1 3rd Qu.:0 3rd Qu.: 0 3rd Qu.:0
Max. :1 Max. :1 Max. : 2 Max. :0
NA's :9579373 NA's :13678889 NA's :13678889 NA's :13678889
P_NFE AF_FIN BETA_FIN SE_FIN
Min. :0 Min. :0 Min. :-15 Min. : 0
1st Qu.:0 1st Qu.:0 1st Qu.: 0 1st Qu.: 0
Median :0 Median :0 Median : 0 Median : 0
Mean :0 Mean :0 Mean : 0 Mean : 0
3rd Qu.:1 3rd Qu.:0 3rd Qu.: 0 3rd Qu.: 0
Max. :1 Max. :1 Max. : 33 Max. :31
NA's :13678889 NA's :6694140 NA's :6694140 NA's :6694140
P_FIN
Min. :0
1st Qu.:0
Median :0
Mean :0
3rd Qu.:1
Max. :1
NA's :6694140