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 1.4.1 Index]