preprocess: preprocessing GSE data from CEL files and series matrix file

In allenaigit/pathwayko: PathwayKO: An R package for knock-out pathway enrichment analysis

preprocessing GSE data from CEL files and series matrix file

Description

This function reads in relevant CEL files (from *_RAW.tar) file and series matrix file (*_series_matrix.txt.gz) typically obtained from NCBI database for a given GSE. The preprocessing of these data relies on the user to interactively provide necessary information as such information is difficult to obtain prior to execution and hence to automate. Reference: Carvalho B.S. and Irizarry R.A. (2010) A framework for oligonucleotide microarray preprocessing. Bioinformatics, 16, 2363–2367; Ritchie M.E., et al. (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res, 43, e47.

Usage

preprocess()

Details

To begin, the user is expected to have obtained '*_RAW.tar' and '*_series_matrix.txt.gz' files of a given GSE. The user will first be asked to choose from files under the working directory with matching suffix as input files. Then the user will be asked to provide relevant information such as keywords for case/control and KO gene names to build experiment design for packages like 'oligo' and 'limma'. The final resault will be saved as an compressed R object to be read in and used by other parts of the package.

Value

TRUE when successful, FALSE otherwise

allenaigit/pathwayko documentation built on Nov. 23, 2022, 5:43 p.m.