Description Usage Value Author(s) Examples
Returns a vector of Ensembl ids of hypoxia related genes.
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Vector of ensembl ids.
Natalie R. Davidson
1 2 3 4 5 6 7 8 9 10 11 12 13 | # 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,]
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