make phenotype tibble for write_cls
make_phenotype(matrix, chip, gene)tibble. usually the return value of rGEO::read_gse_matrix()
tibble. usually the return value of rGEO::read_gse_soft()
character. HUGO gene symbol of your interested gene
tibble. each column represents a phenotype, its name is the phenotype's name (hugo gene symbol), its value contains expression value of all samples in the .txt file
max(c(NA,NA), na.rm = TRUE) produces -Inf
reject too many NA
if (sum(is.infinite(value)) / length(value) <= 0.25) {}
testthat::test_that('make_gsea_input()', {
dataset <- gse51280
gene <- 'ANKLE2'
output_file <- 'tests/testthat/output/GSE51280'
testthat::expect_true(make_gsea_input(dplyr::mutate_at(dataset, 3:4, .
testthat::expect_false(make_gsea_input(dplyr::mutate_at(dataset, 3:10, .
});
NULL
#> NULL