BMfinder {vasp} | R Documentation

## Discover bimodal distrubition features

### 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),]

[Package vasp version 0.99.26 Index]