translate_data: Translation of the rownames IDs of a SummarizedExperiment to...

In babelomics/hipathia: HiPathia: High-throughput Pathway Analysis

Translation of the rownames IDs of a SummarizedExperiment to Entrez IDs.

Description

Translates the IDs in the rownames of a SummarizedExperiment to Entrez IDs. For accepted IDs to be transformed see the DOCUMENTATION.

Usage

translate_data(data, species, sel_assay = 1, verbose = TRUE)

Arguments

data	Either a SummarizedExperiment object or a matrix of gene expression.
species	Species of the samples.
sel_assay	Character or integer, indicating the assay to be translated in the SummarizedExperiment. Default is 1.
verbose	Boolean, whether to show details about the results of the execution.

Value

Either a SummarizedExperiment or a matrix (depending on the input type) of gene expression with Entrez IDs as rownames.

Examples

data("brca_data")
trans_data <- translate_data(brca_data, "hsa")

babelomics/hipathia documentation built on July 27, 2022, 2:23 p.m.