read_affymetrix {autonomics}

R Documentation

Read affymetrix microarray

Description

Read affymetrix microarray

Usage

read_affymetrix(celfiles)

Arguments

celfiles

string vector: CEL file paths

Value

RangedSummarizedExperiment

Examples

require(magrittr)
url <- paste0('http://www.bioconductor.org/help/publications/2003/',
                'Chiaretti/chiaretti2/T33.tgz')
localdir  <- file.path(rappdirs::user_cache_dir(appname = 'autonomics'), 'T33')
dir.create(localdir, showWarnings=FALSE)
localfile <- file.path(localdir, basename(url))
if (!file.exists(localfile)){
    download.file(url, destfile = localfile)
    untar(localfile, exdir = path.expand(localdir))
}
localfile %<>% substr(1, nchar(.)-4)
if (!requireNamespace("BiocManager", quietly = TRUE))  install.packages(
                                                            'BiocManager')
if (!requireNamespace("hgu95av2.db", quietly = TRUE))  BiocManager::install(
                                                            'hgu95av2.db')
# read_affymetrix(celfiles = list.files(localfile, full.names = TRUE))
# currently openblas issue: https://stackoverflow.com/questions/61629861/

---