get_hypoxia_genes {ssPATHS} | R Documentation |
Returns a vector of Ensembl ids of hypoxia related genes.
get_hypoxia_genes()
Vector of ensembl ids.
Natalie R. Davidson
# read in the reference expression data for hypoxia score generation data(tcga_expr_df) # transform from data.frame to SummarizedExperiment tcga_se <- SummarizedExperiment(t(tcga_expr_df[ , -(1:4)]), colData=tcga_expr_df[ , 2:4]) colnames(tcga_se) <- tcga_expr_df$tcga_id colData(tcga_se)$sample_id <- tcga_expr_df$tcga_id # let's get the expression of hypoxia associated genes hypoxia_gene_ids <- get_hypoxia_genes() hypoxia_gene_ids <- intersect(hypoxia_gene_ids, rownames(tcga_se)) hypoxia_se <- tcga_se[hypoxia_gene_ids,]