BMfinder {VaSP} | R Documentation |
Find bimodal distrubition features and divide the samples into 2 groups by k-means clustering.
BMfinder(x, p.value = 0.01, maf = 0.05, miss = 0.05, fold = 2, log = FALSE, cores = detectCores() - 1)
x |
a numeric matrix with feature rows and sample columns, e.g.,
splicing score matrix from |
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 |
The matrix contains 1, 2 and NA, and values of 'x' in group 2 are larger than group 1.
a matrix with feature rows and sample columns.
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),]