gcContent {ORFik} | R Documentation |
0.5 means 50
gcContent(seqs, fa)
seqs |
a character vector of ranges, or ranges as GRangesList |
fa |
fasta index file .fai file, either path to it, or the loaded FaFile, default (NULL), only set if you give ranges as GRangesList |
a numeric vector of gc content scores
# Usually the ORFs are found in orfik, which makes names for you etc. # Here we make an example from scratch seqName <- "Chromosome" ORF1 <- GRanges(seqnames = seqName, ranges = IRanges(c(1007, 1096), width = 60), strand = c("+", "+")) ORF2 <- GRanges(seqnames = seqName, ranges = IRanges(c(400, 100), width = 30), strand = c("-", "-")) ORFs <- GRangesList(tx1 = ORF1, tx2 = ORF2) ORFs <- makeORFNames(ORFs) # need ORF names # get path to FaFile for sequences faFile <- system.file("extdata", "genome.fasta", package = "ORFik") gcContent(ORFs, faFile)