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)

Arguments

seq Character vector.

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 names A, C, T, G, and the values in each column are the counts of the corresponding bases in the elements of x.

Author(s)

R. Gentleman, W. Huber

See Also

complementSeq,reverseSeq

Examples

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

[Package matchprobes version 1.2.1 Index]