injectSNPsMAF {ramwas} | R Documentation |
Injects SNPs from a VCF count file into a DNA sequence.
injectSNPsMAF(gensequence, frqcount, MAF = 0.01)
gensequence |
A string or |
frqcount |
File name of the allele count file produced by
|
MAF |
SNPs with minor allele frequency at or above |
Returns a string with the genome sequence with SNPs injected.
Andrey A Shabalin andrey.shabalin@gmail.com
See injectSNPs
for the standard analog
function without MAF filtering.
gensequence1 = "AAAACAAAA" frqcount = c( "CHROM\tPOS\tN_ALLELES\tN_CHR\t{ALLELE:COUNT}", "1\t6\t2\t1000\tA:400\tG:600", "1\t7\t2\t1000\tA:800\tC:200", "1\t9\t2\t1000\tA:900\tG:100") MAF = 0.01 gensequence2 = injectSNPsMAF(gensequence1, frqcount, MAF) ### No CpGs without SNPs show(gensequence1) getCpGsetCG(gensequence1) ### SNPs create 1 CpG show(gensequence2) getCpGsetALL(gensequence2)