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@nachocab
Last active October 8, 2015 17:26
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Using yaml to deal with gene sets in R
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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