sliceFileSet: Slice a fileSet with samples and probes

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Slice a fileSet with samples and probes

Description

Slice a fileSet with samples and probes

Usage

sliceFileSet(fset, samples = fset$samples, probes = fset$probes, memmax = 10^5)

Arguments

fset	a sesame::fileSet, as obtained via readFileSet
samples	samples to query (default to all samples)
probes	probes to query (default to all probes)
memmax	maximum items to read from file to memory, to protect from accidental memory congestion.

Value

a numeric matrix of length(samples) columns and length(probes) rows

Examples

## create two samples
fset <- initFileSet('mybetas2', 'HM27', c('s1','s2'))

## a hypothetical numeric array (can be beta values, intensities etc)
hypothetical <- setNames(runif(fset$n), fset$probes)

## map the numeric to file
mapFileSet(fset, 's1', hypothetical)

## get data
sliceFileSet(fset, 's1', 'cg00000292')

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.