Description Usage Arguments Value Author(s) See Also Examples
Injects SNPs from a VCF count file into a DNA sequence.
1 | 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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)
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