BMfinder: Discover bimodal distrubition features

In yuhuihui2011/VaSP: Quantification and Visualization of Variations of Splicing in Population

Description

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

Usage

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

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),]

yuhuihui2011/VaSP documentation built on Jan. 11, 2022, 11:21 a.m.