exprFinder {CHARGE} | R Documentation

## exprFinder

### 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%")

[Package CHARGE version 1.2.0 Index]