plink格式数据（ped文件第5列、第6列）
001、ped文件第5列：表示性别信息（1表示male、2表示female、0或者其他字母表示未知）
root@DESKTOP-1N42TVH:/home/test3# ls outcome.map outcome.ped root@DESKTOP-1N42TVH:/home/test3# cat outcome.ped ## 测试数据， 第5列 DOR 1 0 0 0 9 G G C C G G G G A G A A DOR 2 0 0 ewr 9 G G G C G G G G G G A A DOR 3 0 0 1 19 G G C C G G G G G G A A DOR 4 0 0 2 39 G G C C G G G G G G A A DOR 5 0 0 2 93 G G C C G G G G G G A A DOR 6 0 0 kku -9 G G C C G G G G G G A A root@DESKTOP-1N42TVH:/home/test3# plink --file outcome --recode tab --out outcome; rm *.log *.nosex 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 outcome.log. Options in effect: --file outcome --out outcome --recode tab 16007 MB RAM detected; reserving 8003 MB for main workspace. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (6 variants, 6 people). --file: outcome-temporary.bed + outcome-temporary.bim + outcome-temporary.fam written. 6 variants loaded from .bim file. 6 people (1 male, 2 females, 3 ambiguous) loaded from .fam. ## 1个male，2个female，0或者其他表示未知 Ambiguous sex IDs written to outcome.nosex . 5 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, 6 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is exactly 1. 6 variants and 6 people pass filters and QC. Phenotype data is quantitative. --recode ped to outcome.ped + outcome.map ... done. root@DESKTOP-1N42TVH:/home/test3# cat outcome.ped ## 第5列性别未知的情况下，自动转换为了0 DOR 1 0 0 0 9 G G C C G G G G A G A A DOR 2 0 0 0 9 G G G C G G G G G G A A DOR 3 0 0 1 19 G G C C G G G G G G A A DOR 4 0 0 2 39 G G C C G G G G G G A A DOR 5 0 0 2 93 G G C C G G G G G G A A DOR 6 0 0 0 -9 G G C C G G G G G G A A
002、ped文件第6列表示表型，-9或者其他字符表示缺失。
root@DESKTOP-1N42TVH:/home/test3# ls outcome.map outcome.ped root@DESKTOP-1N42TVH:/home/test3# cat outcome.ped ## 测试数据，第6列表示性别，-9或者其他字符表示缺失 DOR 1 0 0 0 9 G G C C G G G G A G A A DOR 2 0 0 0 9 G G G C G G G G G G A A DOR 3 0 0 1 19 G G C C G G G G G G A A DOR 4 0 0 2 kku G G C C G G G G G G A A DOR 5 0 0 2 ewr G G C C G G G G G G A A DOR 6 0 0 0 -9 G G C C G G G G G G A A root@DESKTOP-1N42TVH:/home/test3# plink --file outcome --recode tab --out outcome; rm *.log *.nosex 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 outcome.log. Options in effect: --file outcome --out outcome --recode tab 16007 MB RAM detected; reserving 8003 MB for main workspace. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (6 variants, 6 people). --file: outcome-temporary.bed + outcome-temporary.bim + outcome-temporary.fam written. 6 variants loaded from .bim file. 6 people (1 male, 2 females, 3 ambiguous) loaded from .fam. Ambiguous sex IDs written to outcome.nosex . 3 phenotype values loaded from .fam. ## -9或者其他字符表示缺失 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, 6 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is exactly 1. 6 variants and 6 people pass filters and QC. Phenotype data is quantitative. --recode ped to outcome.ped + outcome.map ... done. root@DESKTOP-1N42TVH:/home/test3# cat outcome.ped ## 表型缺失自动转换为了-9 DOR 1 0 0 0 9 G G C C G G G G A G A A DOR 2 0 0 0 9 G G G C G G G G G G A A DOR 3 0 0 1 19 G G C C G G G G G G A A DOR 4 0 0 2 -9 G G C C G G G G G G A A DOR 5 0 0 2 -9 G G C C G G G G G G A A DOR 6 0 0 0 -9 G G C C G G G G G G A A
小结：
001、ped文件的第5列表示性别：1表示male； 2表示female； 0或者其他任意字符表示未知，默认缺失为0.
002、ped文件的第6列表示表型：-9或者其他任意字符表示缺失，默认缺失为-9.
