plink软件计算基因频率产生NA的原因
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root@PC1:/home/test# ls outcome.map outcome.ped root@PC1:/home/test# cat outcome.map ## 测试数据map文件 20 OAR20_27119.1 0 217914 20 OAR20_192404.1 0 308307 21 OAR21_338481.1 0 230847 21 OAR21_369726.1 0 262607 22 OAR22_728735.1 0 260996 22 OAR22_832781.1 0 363750 23 OAR23_393569_X.1 0 299533 23 OAR23_429075.1 0 335259 24 s75016.1 0 56233 24 s72739.1 0 96354 25 s33329.1 0 83221 25 DU455254_479.1 0 100959 26 OAR26_222715_X.1 0 165273 26 OAR26_291834.1 0 205049 root@PC1:/home/test# plink --file outcome --freq --out result &>/dev/null; rm *.log *.nosex root@PC1:/home/test# ls outcome.map outcome.ped result.frq root@PC1:/home/test# cat result.frq ## 查看结果 CHR SNP A1 A2 MAF NCHROBS 20 OAR20_27119.1 A C 0.125 880 20 OAR20_192404.1 G A 0.3057 880 21 OAR21_338481.1 A G 0.4 880 21 OAR21_369726.1 C A 0.4148 880 22 OAR22_728735.1 C A 0.09432 880 22 OAR22_832781.1 A G 0.4057 880 23 OAR23_393569_X.1 A G 0.4068 880 23 OAR23_429075.1 G A 0.3011 880 24 s75016.1 0 C NA 0 24 s72739.1 G A NA 0 25 s33329.1 A G 0.167 880 25 DU455254_479.1 A G 0.1602 880 26 OAR26_222715_X.1 A G 0.4614 880 26 OAR26_291834.1 G A 0.2795 880
产生NA的原因在于计算物种的染色体数目有24; 24号染色体的数据, plink计算默认全部生成为NA。