get_GO_exp: Preprocess Gene Expression

Description Usage Arguments Examples

Description

This function reduces the gene expression matrix to selected Gene Ontology genes.

Usage

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get_GO_exp(gene_cell_matrix, gene_type = "gene_names",
  organism = "mouse", takelog = T)

Arguments

gene_cell_matrix

A genes (row) by cells (col) matrix.

gene_type

The type of gene names. Default is "gene_names" - ie "HOPX", alternatively "entrez" is provided.

organism

The type of species the dataset belongs to: defaults to "mouse". "human" option is available.

takelog

Defaults to TRUE. Whether to perform log2(exprs + 1)

Examples

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subset_GO_data <- get_GO_exp(data, gene_type = "gene_names", organism = "human", takelog = F)
filtered_GO_data <- filter_exp(subset_GO_data, dispersion_threshold = 10, threads = 2)

tinglab/redPATH documentation built on May 31, 2019, 10:37 a.m.