genoset-subset: Subset a GenoSet

In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description

Subset a GenoSet

Usage

## S4 method for signature 'GenoSet,ANY,ANY,ANY'
x[i, j, k, ..., withDimnames = TRUE,
  drop = FALSE]

## S4 replacement method for signature 'GenoSet,ANY,ANY,ANY'
x[i, j, k] <- value

Arguments

x	GenoSet
i	character, GRanges, logical, integer
j	character, logical, integer
k	character or integer
...	additional subsetting args
withDimnames	scalar logical, put dimnames on returned assay?
drop	logical drop levels of space factor?
value	incoming data for assay 'k', rows 'i' and cols 'j'

Examples

  data(genoset,package='genoset')
  genoset.ds[1:5,2:3]  # first five probes and samples 2 and 3
  genoset.ds[ , 'K']  # Sample called K
  gr = GRanges(ranges=IRanges(start=seq(from=15e6,by=1e6,length=7),width=1,names=letters[8:14]),seqnames=rep('chr17',7))
  genoset.ds[ gr, 'K' ]  # sample K and probes overlapping those in rd, which overlap specifed ranges on chr17

genoset documentation built on Nov. 8, 2020, 6:07 p.m.