exprFinder: exprFinder

In BenjaminAdelaide/CHARGE: CHARGE: CHromosome Assessment in R from Gene Expression data

Description

Performs a bimodality test at multiple defined bin sizes across the genome using a sliding window approach.

Usage

exprFinder(se, ranges, binWidth, binStep, threshold = NULL, threads = 1)

Arguments

se	A SummarizedExperiment containing the nromalised gene expression data.
ranges	A GRanges object containing the genomic regions to scan.
binWidth	The length of each bin.
binStep	The distance the bin will slide.
threshold	Optional. The quantile threshold of expression variation of genes to be used at each bin. Default is NULL.
threads	Total number of threads to be used. Default is 1.

Details

Uses a sliding window approach to scan over a defined genomic region. It automatically performs a bimodal test and calculates Hartigan's dip test statistic for unimodality and returns a data frame listing each bin and the statistical likelihood of a duplication or deletion.

Value

Returns a data frame containing the genomic locations of each bin and bimodality statistics.

Author(s)

Benjamin Mayne

Examples

library(GenomicRanges)
library(EnsDb.Hsapiens.v86)
data(datExprs)
chr21 <- GRanges("21:1-46709983")
chrLengths <- GRanges(seqinfo(EnsDb.Hsapiens.v86)[c("21", "22", "Y")])
exprFinder.out <- exprFinder(se = datExprs, ranges = chrLengths,
binWidth = 1e+9, binStep = 1e+9, threshold = "25%")

BenjaminAdelaide/CHARGE documentation built on May 14, 2019, 6:04 a.m.