BMfinder: Discover bimodal distrubition features

Description Usage Arguments Details Value Examples

View source: R/BMfinder.R

Description

Find bimodal distrubition features and divide the samples into 2 groups by k-means clustering.

Usage

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BMfinder(x, p.value = 0.01, maf = 0.05, miss = 0.05, fold = 2, log = FALSE, 
        cores = detectCores() - 1)

Arguments

x

a numeric matrix with feature rows and sample columns, e.g., splicing score matrix from spliceGenome or spliceGene function.

p.value

p.value threshold for bimodal distrubition test

maf

minor allele frequency threshold in k-means clustering

miss

missing grouping rate threshold in k-means clustering

fold

fold change threshold between the two groups

log

whether the scores are to be logarithmic. If TRUE, all the scores are log2 tranformed before k-means clustering: x = log2(x+1).

cores

threads to be used. This value is passed to ?mclapply in parallel package

Details

The matrix contains 1, 2 and NA, and values of 'x' in group 2 are larger than group 1.

Value

a matrix with feature rows and sample columns.

Examples

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data(rice.bg)
score<-spliceGene(rice.bg,'MSTRG.183',junc.type='score')
score<-round(score,2)
as<-BMfinder(score,cores=1) # 4 bimodal distrubition features found

##compare
as
score[rownames(score)%in%rownames(as),]

VaSP documentation built on Feb. 28, 2021, 2:02 a.m.