determine_abundance: Determine the abundance of integration sites within a GRanges...

In cnobles/gintools: Genomic DNA Integration Analysis Tools

Description

Given a GRanges object containing the genomic ranges of flanking genomic DNA from integration sites, the function returns abundance information based on unique widths for each site (method = "fragLen", default) or applies a more powerful tool developed in sonicLength package (method = "estAbund"). If multiple samples are given, they can be grouped separately by giving the metadata column to the grouping option.

Usage

determine_abundance(sites)

determine_abundance(sites, grouping = NULL, replicates = NULL,
method = "fragLen")

Arguments

sites	GRanges object with flanking genomic DNA ranges.
grouping	Character name of the metadata column with grouping information.
replicates	Character name of the metadata column which dictates replicate information.
method	Character either "fragLen" for determining abundance by unique fragment length or "estAbund" to use the sonicLength package.

Details

determine_abundance returns the abundance of all distinct integration sites within the given GRanges object based on the unique fragment length (width) or utilizes the sonicLength package.

Author(s)

Christopher Nobles, Ph.D.

Examples

gr <- gintools:::generate_test_granges()
std.gr <- standardize_sites(gr)

determine_abundance(std.gr)

cnobles/gintools documentation built on Aug. 22, 2019, 10:36 a.m.