read_affymetrix: Read affymetrix microarray

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Read affymetrix microarray

Description

Read affymetrix microarray

Usage

read_affymetrix(celfiles)

Arguments

celfiles

string vector: CEL file paths

Value

RangedSummarizedExperiment

Examples

# Downloading example dataset fails 600s limit - example outcommented.
# url <- paste0('http://www.bioconductor.org/help/publications/2003/Chiaretti/chiaretti2/T33.tgz')
# localdir  <- file.path(tools::R_user_dir('autonomics', 'cache'), '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))

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.