get_hypoxia_genes {ssPATHS} | R Documentation

## Get Ensembl ids of hypoxia related genes.

### Description

Returns a vector of Ensembl ids of hypoxia related genes.

### Usage

    get_hypoxia_genes()

### Value

Vector of ensembl ids.

### Author(s)

Natalie R. Davidson

### Examples

    # 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,]

[Package ssPATHS version 1.2.0 Index]