bimodalTest: bimodalTest

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

Description

Performs a bimodal test and calcualtes Hartigan's statistic and p-value over a genomic region of interest using gene expression data set, the output from cvExpr.

Usage

bimodalTest(se, cvExpr, threshold = NULL)

Arguments

se	A SummarizedExperiment containing the normalised gene expression data.
cvExpr	The output from cvExpr.
threshold	Optional. The quantile threshold of genes to be used for clustering analaysis. Default is NULL.

Details

Performs a bimodal test and calculates Hartigan's dip test statistic for unimodality for a given gene expression data set. A bimodality coefficient value > 5/9 suggests bimodality and the closer the bimodality ratio is to 1, the more evenly distrubted the data set. The dip statistic and p-value can be used to determine if the region of interest is statistically significant.

The second part of the function returns the Z score means which can be used to visualise the denisty or distribution of the samples.

Value

Returns a list containing the output from the bimodal test.

Author(s)

Benjamin Mayne

Examples

library(GenomicRanges)
data(datExprs)
chr21 <- GRanges("21:1-46709983")
cvExpr.out <- cvExpr(se = datExprs, region = chr21)
bimodalTest.out <- bimodalTest(se = datExprs, cvExpr = cvExpr.out, threshold = "25%")

CHARGE documentation built on April 28, 2020, 6:06 p.m.