ufeatByTiling: split featurenames of SummarizedExperiment according to...

In gQTLBase: gQTLBase: infrastructure for eQTL, mQTL and similar studies

Description

split featurenames of SummarizedExperiment according to tiling, without redundancies

Usage

ufeatByTiling(se, tiling, maxlen=20)
balancedFeatList(se, maxlen=20)

Arguments

se	instance of SummarizedExperiment
tiling	GRanges instance corresponding to a genomic tiling
maxlen	numeric ... list elements longer than maxlen are chopped up to have this length, to foster load balancing

Details

ufeatByTiling uses findOverlaps, balancedFeatList uses split on seqnames and BBmisc::chunk

Value

a list with elements of names(rowRanges(se)) corresponding to the elements of the tiling

Examples

## Not run: 
library(geuvPack)
data(geuFPKM)
library(Homo.sapiens)
au = paste0("chr", 1:22)
tg_500k = tileGenome(seqinfo(TxDb(Homo.sapiens))[au,], tilewidth=500000,
  cut.last.tile.in.chrom=TRUE)
sn = ufeatByTiling(geuFPKM, tg_500k)
summary(sapply(sn,length))
sn2 = balancedFeatList(geuFPKM)
summary(sapply(sn2,length))

## End(Not run)

gQTLBase documentation built on Nov. 8, 2020, 7:07 p.m.