im_cor_tcga: Finds Spearman correlation between an oncogene, an immune...

In Bozorgui/imogene: : Immuno-oncology gene expression associations

Description

Finds Spearman correlation between an oncogene, an immune checkpoint and immune associated phenotypes.

Usage

im_cor_tcga(onco_gene, icp_gene, cohort, sample_list)

Arguments

onco_gene	A character vector of gene Hugo symbols.
icp_gene	An optional character vector of immune checkpoint gene/protein IDs.
cohort	a character vector of TCGA diseases
sample_list	An optional character vector of TCGA samples barcodes indicating a subset of samples within a cohort.

Details

im_cor_tcga uses NASeq2GeneNorm expression data, as provided by curatedTCGAData, to find correlation between onco_genes and immune checkpoints and immuno-oncology features as listed in TCGA_immune_features_list.

By default (if no icp_gene is specified), icp_gene_list will be used.

For TCGA disease list see TCGA_disease_list

All barcodes in sample_list must be 15 character long and belong to the same cohort. When sample_list is provided, cohort should be the disease cohort that they belong to, otherwise only the first element of the cohort list will be used.

A non-FDR-adjusted p.value is reported for each correlation value to allow for easier adjustments by user.

All barcodes in sample_list must be 15 character long and belong to the same cohort. When sample_list is provided, cohort should be the disease cohort that they belong to, otherwise only the first element of the cohort list will be used.

Value

a list of dataframes containing Spearman correlations and non-FDR adjusted probability values.

Examples

im_cor_tcga(onco_gene=c("BRAF"),icp_gene=c("CD274","CTLA4"),cohort=c("gbm"))

Bozorgui/imogene documentation built on Feb. 21, 2022, 11:57 a.m.