Skip to contents

Calculate GC content of coding sequences

Source: R/gene_index.R
get_gc.Rd

get_gc calculates the overall GC content (percentage of guanine and cytosine nucleotides) for each coding sequence.

Usage

get_gc(cf)

Arguments

cf

A matrix of codon frequencies as calculated by count_codons(). Rows represent sequences and columns represent codons.

Value

A named numeric vector of GC content values (ranging from 0 to 1). Names correspond to sequence identifiers from the input matrix.

Examples

# Calculate GC content for yeast genes
cf_all <- count_codons(yeast_cds)
gc <- get_gc(cf_all)
head(gc)
#>   YPL071C   YLL050C   YMR172W   YOR185C   YLL032C   YBR225W 
#> 0.3566879 0.3981481 0.4101852 0.4027149 0.3454399 0.3880873 
hist(gc, main = "Distribution of GC content")