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=== Multiple testing correction === '''multtest_R.R'''<br> source("http://bioconductor.org/biocLite.R") biocLite("multtest") library(multtest) A=read.table("sorted_SNP-CpG_pval_UCLA_SZ_SeqDepTest_TTest_minpval0.05.txt",header=TRUE) B=A$p_ttest p_adj=p.adjust(B, method = "BH", n = 73,271) summary(p_adj) write.table(file="UCLA_SZ_SeqDepTest_TTest_pval2qval_p.adjust.BH.txt", p_adj, append = FALSE,row.names = FALSE) * I decided to selected the SNP-CpG ASM with FDR < 20% as Dr. Zhang said that it is still acceptable even 5% FDR is ideal. Total I got 8,646 candidate ASM. * Sort out the original ASM_TTest matrix based on the p-value sort -g -k98 UCLA_SZ_SeqDepTest_TTest_PVal0.05.txt > sorted_UCLA_SZ_SeqDepTest_TTest_PVal0.05.txt * Print out the ASM that have FDR <= 10% and 20% head -8336 sorted_UCLA_SZ_SeqDepTest_TTest_PVal0.05.txt > 10%FDR_sorted_UCLA_SZ_SeqDepTest_TTest.txt (8,335 sites, min p-value ~ 0.01142...) head -8647 sorted_UCLA_SZ_SeqDepTest_TTest_PVal0.05.txt > 20%FDR_sorted_UCLA_SZ_SeqDepTest_TTest.txt (8,646, min p-value ~ 0.02358...) * Extract number of significant ASM ** SNP-free ASM: 665 sites (8%) ** SNP on CpG ASM: 7,670 sites (92%) ./getnoSNPCpG_edit.pl 10%FDR_sorted_UCLA_SZ_SeqDepTest_TTest.txt > 10%FDR_noSNPonCpG_UCLA_SeqDep_TTest.txt ./getSNPonCpG.pl 10%FDR_sorted_UCLA_SZ_SeqDepTest_TTest.txt > 10%FDR_SNPonCpG_UCLA_SeqDep_TTest.txt
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