basecontent {matchprobes}R Documentation

Obtain the ATCG content of a gene

Description

This function accepts a character vector representing the nucleotide sequences and computes the frequencies of each base (A, C, G, T).

Usage

basecontent(seq)
countbases(seq, dna = TRUE)

Arguments

seq Character vector.
dna Logical value indicating whether the sequence is DNA (TRUE) or RNA (FALSE)

Details

The base frequencies are calculated separately for each element of x. The elements of x can be in upper case, lower case or mixed.

Value

A matrix with 4 columns and length(x) rows. The columns are named A, C, T, G, and the values in each column are the counts of the corresponding bases in the elements of x. When dna=FALSE, the T column is replaced with a U column.

Author(s)

R. Gentleman, W. Huber, S. Falcon

See Also

complementSeq,reverseSeq, revcompDNA, revcompRNA

Examples

 v<-c("AAACT", "GGGTT", "ggAtT")
 basecontent(v)

 countbases(v)

[Package matchprobes version 1.14.1 Index]