summarize_by_gene_symbol: Summarize Matrix

In RGLab/HIPCMatrix: Microarray and RNA-seq Processing for ImmuneSpace

Summarize Matrix

Description

Summarize any duplicated genes so that there is one entry per gene.

Usage

summarize_by_gene_symbol(
  ge_dt,
  feature_gene_map,
  method = "mean",
  verbose = FALSE
)

Arguments

ge_dt	data.table of gene expression values. Features should be listed in feature_id column, with additional columns for each sample. Samples should be labelled by biosample id.
feature_gene_map	data.table mapping original gene id (eg probe id, ensembl id, gene alias) to gene symbol. It should have two columns: featureid (original) and genesymbol (updated).
method	Summarization method. mean or max. mean will return the mean of all features mapping to a gene alias for each sample. This is the method used in the ImmuneSpace HIPCMatrix pipeline. max will chose the probe which has the greatest geometric mean expression across all samples. This is the method used in the ImmuneSignatures analysis.
verbose	write verbose logging statements?

Details

This function summarizes normalized expression values by mean into a table with one entry per gene name based on feature_gene_map. The input data should be in log2 space.

RGLab/HIPCMatrix documentation built on Jan. 29, 2023, 5:13 a.m.