library("data.table") library("Biostrings") library("pseudoRef") arules <- data.frame(from=c("M", "Y", "R", "K"), to=c("C", "C", "G", "T")) h <- read.table("head.txt", header=TRUE) snpdt <- fread("n1000_bisnp_annot.txt", header=FALSE) names(snpdt) <- gsub("_.*", "", names(h)) # fa can be "character", "DNAStringSet" or "DNAString" fa <- "sample_chr10.fa" fa <- readDNAStringSet(filepath = fa, format="fasta") pseudoRef(fa, snpdt, sidx = 5:6, arules, outdir="output")
fa <- readDNAStringSet(filepath = "sample_chr10.fa", format="fasta") fa2 <- readDNAStringSet(filepath = "output/JRIAL2A.fasta", format="fasta") sub <- snpdt[JRIAL2A != "./." & ref != JRIAL2A][, 1:5] p <- 275 subseq(fa[1], sub$pos[p], sub$pos[p]) subseq(fa2[1], sub$pos[p], sub$pos[p])
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