oligonucleotideFrequencyByChromosome: Find oligonucleotide frequencies for multiple chromosomes

In seandavi/Rpressa: A collection of useful code for bioinformatics

Description

The oligonucleotideFrequency function is useful for finding things like GC percentage, etc., from a DNAString object (or others). However, if one wants to use the combination of BSgenome and oligonucleotideFrequency to find these parameters over the genome, this is a tedious process. This little function streamlines the process for doing things like finding the GC percentage of probes or regions across the entire genome of interest.

Usage

oligonucleotideFrequencyByChromosome(chromosome, start, end, BSgenomeObject, width = 1)

Arguments

chromosome	A character vector of the chromosome of each region. The vector members need to match the names used in the BSgenome data package (typically, these are going to look like the UCSC chromosomes, "chr1", "chr2", ....)
start	An integer vector (1-based) of the start locations for the oligonucleotide frequency calculations. Start locations that, for whatever reason, are less than 1 are set to 1.
end	An integer vector (1-based) of the end locations for the oligonucleotide frequency calculations. End locations that, for whatever reason, are greater than the length of the respective chromosome are set to the length of the chromosome.
BSgenomeObject	The BSgenome object. For example, if the genome of interest is drawn from the "BSgenome.Hsapiens.UCSC.hg18", then the variable that holds the genome sequences is Hsapiens. It is this actual variable that should be used here.
width	Integer value describing the width of the nmers to check (1 for A, C, T, G; 2 for dinucleotides; etc.)

Value

An integer matrix with the counts of oligonucleotides, one row for each location, in the same order as the input chromosome, start, end.

Author(s)

Sean Davis <[e-mail]>

See Also

oligonucleotideFrequency

Examples

require(BSgenome)
require(BSgenome.Hsapiens.UCSC.hg18)
oligonucleotideFrequencyByChromosome(chromosome=c('chr1','chr2','chr3'),
                                     start=c(1,1,1),
                                     end=c(10000,10000,9000),
                                     BSgenomeObject=Hsapiens,
                                     width=2)

seandavi/Rpressa documentation built on May 29, 2019, 4:33 p.m.