get_specific_gene_exprs: Search for specific gene expression

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

Description

Gets the subset of genes which resemble the enquired gene name within the dataset. This prepares for the plotting function of multiple gene expressions along the pseudo development time.

Usage

get_specific_gene_exprs(full_gene_exprs_matrix, gene_name = "cdk",
  type = "grep", organism = "mm")

Arguments

full_gene_exprs_matrix	This is the full gene (row) by cell (col) matrix of your dataset.
gene_name	The gene name that is desired / enquired.
type	pattern matching "grep" or exact "match"
organism	"mm" for Mouse or "hs" for Human

Examples

cdk_gene_exprs <- get_specific_gene_exprs(full_gene_exprs_data, gene_name = "cdk11", type = "grep", organism = "mm")
plot_cdk <- plot_specific_gene_exprs(cdk_gene_exprs, redpath_pseudotime, color_label = cell_type_label, order = T)
require(scater)
multiplot(plotlist = plot_cdk, layout = matrix(c(1:2), 2, 1)) # For a total number of 2 plots

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