make_phenotype: make phenotype tibble for write_cls
In dongzhuoer/qGSEA: Simplest tool to prepare GSEA input files

Description Usage Arguments Value internal note to do Examples

make phenotype tibble for write_cls

1	make_phenotype(matrix, chip, gene)

`matrix`	tibble. usually the return value of `rGEO::read_gse_matrix()`
`chip`	tibble. usually the return value of `rGEO::read_gse_soft()`
`gene`	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, . });