exprFinder {CHARGE} | R Documentation |
Performs a bimodality test at multiple defined bin sizes across the genome using a sliding window approach.
exprFinder(se, ranges, binWidth, binStep, threshold = NULL, threads = 1)
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. |
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.
Returns a data frame containing the genomic locations of each bin and bimodality statistics.
Benjamin Mayne
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%")