可能是你的数据问题,没有明显的群体分层
老师您好,我算了五组数据,结果的CV值都随着K增大而递增,用的是群体遗传进化课程中docker的代码,如下:
workdir=/work #设置工作路径
refdir=$workdir/ref
datadir=$workdir/data
scriptdir=$workdir/scripts
export PATH=$scriptdir:$PATH
GROUP=$datadir/yuan.txt
#LD过滤
plink --vcf $workdir/00.filter/YuanJiang.vcf.gz --indep-pairwise 50 10 0.2 --out ld \
--allow-extra-chr --set-missing-var-ids @:#
#提取
plink --vcf $workdir/00.filter/YuanJiang.vcf.gz --make-bed --extract ld.prune.in \
--out LDfiltered --recode vcf-iid --keep-allele-order --allow-extra-chr --set-missing-var-ids @:#
#转换成plink格式
vcftools --vcf LDfiltered.vcf --plink \
--out plink
#转换成admixture要求的bed格式
plink --noweb --file plink --recode12 --out admixture \
--allow-extra-chr --keep-allele-order
#admixture 群体结构分析
for k in {2..8};do
echo "admixture -j2 -C 0.01 --cv admixture.ped $k >admixture.log$k.out"
admixture -j2 -C 0.01 --cv admixture.ped $k >admixture.log$k.out
done
结果基本都这样admixture.log2.out:CV error (K=2): 0.72510
admixture.log3.out:CV error (K=3): 0.89316
admixture.log4.out:CV error (K=4): 0.97867
admixture.log5.out:CV error (K=5): 1.15691
admixture.log6.out:CV error (K=6): 1.33166
admixture.log7.out:CV error (K=7): 1.54018
admixture.log8.out:CV error (K=8): 1.69137
admixture.log2.out:CV error (K=2): 0.60059
admixture.log3.out:CV error (K=3): 0.64067
admixture.log4.out:CV error (K=4): 0.67554
admixture.log5.out:CV error (K=5): 0.71547
admixture.log6.out:CV error (K=6): 0.77872
admixture.log7.out:CV error (K=7): 0.83947
admixture.log8.out:CV error (K=8): 0.90153
五组都是这样递增的,请问是什么情况?