filter_exp: Filter genes

In tinglab/redPATH: Reconstructing the pseudo development time of cell lineages in single cell RNA-Seq data and applications in cancer.

Description

This function reduces the dimensionality by filtering out low dispersion ratio genes.

Usage

filter_exp(cell_gene_matrix, dispersion_threshold = 10, threads = 2)

Arguments

cell_gene_matrix	A cell (row) by gene (col) matrix. Typically the result returned from get_GO_exp.
dispersion_threshold	Defaults to 10. Depending on the type of normalization / data, the ratio should be changed to retain a few hundred genes.
threads	The number of threads to use.

Examples

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.