plink 软件中 --allow-no-sex 参数的作用

--allow-no-sex：在进行关联分析时，缺失性别信息时，仍然进行分析。

001、缺失性别信息，同时不使用改参数时：

root@DESKTOP-1N42TVH:/home/test3# ls
clean.bed  clean.bim  clean.fam
root@DESKTOP-1N42TVH:/home/test3# head -n 5 clean.fam
Line105 Line105 0 0 0 108.668751356079
Line174 Line174 0 0 0 112.071538795501
Line154 Line154 0 0 0 92.6270391416653
Line107 Line107 0 0 0 108.668751356079
Line148 Line148 0 0 0 82.9047893147477
root@DESKTOP-1N42TVH:/home/test3# plink --bfile clean --allow-extra-chr --linear --out result
PLINK v1.90b6.26 64-bit (2 Apr 2022)           www.cog-genomics.org/plink/1.9/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to result.log.
Options in effect:
  --allow-extra-chr
  --bfile clean
  --linear
  --out result

16007 MB RAM detected; reserving 8003 MB for main workspace.
38375 variants loaded from .bim file.
176 people (0 males, 0 females, 176 ambiguous) loaded from .fam.
Ambiguous sex IDs written to result.nosex .
176 phenotype values loaded from .fam.
Warning: Ignoring phenotypes of missing-sex samples.  If you don't want those
phenotypes to be ignored, use the --allow-no-sex flag.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 176 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.931314.
38375 variants and 176 people pass filters and QC.
Note: No phenotypes present.
Warning: Skipping --linear since # variables >= # samples.
root@DESKTOP-1N42TVH:/home/test3# ls
clean.bed  clean.bim  clean.fam  result.log  result.nosex

002、增加该参数

root@DESKTOP-1N42TVH:/home/test3# ls
clean.bed  clean.bim  clean.fam
root@DESKTOP-1N42TVH:/home/test3# plink --bfile clean --allow-extra-chr --linear --allow-no-sex --out result
PLINK v1.90b6.26 64-bit (2 Apr 2022)           www.cog-genomics.org/plink/1.9/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to result.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --bfile clean
  --linear
  --out result

16007 MB RAM detected; reserving 8003 MB for main workspace.
38375 variants loaded from .bim file.
176 people (0 males, 0 females, 176 ambiguous) loaded from .fam.
Ambiguous sex IDs written to result.nosex .
176 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 176 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.931314.
38375 variants and 176 people pass filters and QC.
Phenotype data is quantitative.
Writing linear model association results to result.assoc.linear ... done.
root@DESKTOP-1N42TVH:/home/test3# ls
clean.bed  clean.bim  clean.fam  result.assoc.linear  result.log  result.nosex
root@DESKTOP-1N42TVH:/home/test3# head -n 5 result.assoc.linear
 CHR          SNP         BP   A1       TEST    NMISS       BETA         STAT            P
   1      1:11923      11923    A        ADD      170     0.8928       0.3621       0.7178
   1      1:12127      12127    A        ADD      159     -1.618      -0.6809       0.4969
   1      1:41890      41890    C        ADD      166     -4.173       -5.688    5.755e-08
   1     1:129602     129602    C        ADD      165      -2.79       -1.791      0.07518