get_hypoxia_genes: Get Ensembl ids of hypoxia related genes.

In nrosed/ssPATHS: ssPATHS: Single Sample PATHway Score

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,]

nrosed/ssPATHS documentation built on April 24, 2020, 6:22 p.m.