basecontent {matchprobes}R Documentation

Obtain the ATCG content of a gene

Description

This function accepts a character string representing the base sequence of the DNA for a gene and computes the counts of each base.

Usage

basecontent(seq)

Arguments

seq Character vector.

Details

Each element of x is separately decomposed into its base sequence components.

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.
The elements of x can be in upper case, lower case or mixed.

Author(s)

R. Gentleman, W. Huber

See Also

complementSeq,reverseSeq

Examples

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

[Package matchprobes version 1.0.12 Index]