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Using yaml to deal with gene sets in R
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| install.packages("yaml") | |
| # change path to your favorite local directory | |
| gene_list <- function(filename, format = "yaml", path = "/Users/nacho/gene_info/gene_sets"){ | |
| path <- file.path(path, filename) | |
| if (format == "yaml"){ | |
| raw_genes <- yaml::yaml.load_file(path) | |
| # TODO: run through the nested names in genes and check that | |
| # there are no "." or ":", give warning or replace with "_" | |
| unlisted_genes <- unlist(raw_genes) | |
| groups <- sub("\\d+$", "", names(unlisted_genes)) | |
| genes <- list(nested = tapply(unlisted_genes, groups, unname)) | |
| names(genes$nested) <- gsub('\\.', ':', names(genes$nested)) | |
| genes$flat <- unique(unname(unlist(raw_genes))) | |
| } else { | |
| genes <- scan(path, "character") | |
| } | |
| genes | |
| } | |
| # example usage | |
| my_isgs <- gene_list("isgs.yaml")$flat | |
| [1] "CXCL10" "CXCL11" "DDX58" ... |
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