homoP: Homopolymers in DNA sequences

In spiderDev: Species Identity and Evolution in R--development

Description

Determines the number of homopolymeric series over a certain size within DNA sequences.

Usage

homoP(sequence, num)

Arguments

sequence	DNA sequence
num	Length of homopolymer

Details

Homopolymer series in DNA sequences are stretches of a single base e.g. TAAAAAAACGT. They cause read errors in some next generation sequencing devices such as 454 pyrosequencing due to the chemistry used in these devices. This function allows the number of homopolymeric series in sequences to be counted. When conducted in conjunction with a sliding window analysis, it can help determine which portion of a gene might perform best in a study where NGS may be used.

Value

A value giving the number of homopolymeric series in the sequence.

Author(s)

Samuel Brown <[e-mail]> and Stephane Boyer

Examples

data(dolomedes)

homoP(dolomedes[1,], 4) 

apply(dolomedes, MARGIN = 1, function(x) homoP(x, 4))

spiderDev documentation built on May 2, 2019, 5:23 p.m.