prepare GSEA input files from GSE raw data — make_gsea

You can use first example if you already have a phenotype labels file, or use second example if you are interested in gene sets co-expressing with certain gene(s).

make_gsea_input(matrix_file, soft_file, output_dir = ".", gene = NULL)

Arguments

matrix_file: string. path to GSE series matrix file
soft_file: string. path to GSE SOFT file
output_dir: string, path to output directory
gene: character. HUGO gene symbol(s) of your interested gene(s)

Value

NULL

Details

both NA and Inf are not allowed in input files (.txt & .cls).

Examples

if (FALSE) {
  make_gsea_input(
    system.file('extdata/GSE51280_series_matrix.txt.gz', package = 'rGEO'),
    system.file('extdata/GSE51280_family.soft.gz', package = 'rGEO')
  )

  make_gsea_input(
    system.file('extdata/GSE19161_series_matrix.txt.gz', package = 'rGEO'),
    system.file('extdata/GSE19161_family.soft.gz', package = 'rGEO'),
    '.', 'EIF4G2'
  )
}