gcContent {ORFik}R Documentation

Get GC content

Description

0.5 means 50

Usage

gcContent(seqs, fa)

Arguments

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

Value

a numeric vector of gc content scores

Examples

# 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)

[Package ORFik version 1.4.0 Index]