ufeatByTiling {gQTLBase}R Documentation

split featurenames of SummarizedExperiment according to tiling, or to achieve simple balance within seqnames

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)
[Package gQTLBase version 1.19.0 Index]