gene_selection: Selects significant 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 selects the significant genes from either 1 or 2 correlation vectors

Usage

gene_selection(full_gene_exprs, pseudo_time, correlation_vector,
  correlation_vector2 = NULL, threshold = 0.5)

Arguments

full_gene_exprs	A gene (row) by cell (col) gene expression matrix with all genes.
pseudo_time	The pseudo development time
correlation_vector	The calculated correlation vector of each gene (from calc_correlation)
correlation_vector2	Optional vector to select the significant genes. Defaults to NULL. If provided, genes will be selected if the threshold satisfies either correlation vectors.
threshold	The threshold cut-off to retain significant genes. Defaults to 0.5

Examples

dcor_result <- calc_correlation(full_exprs_matrix, redpath_pseudotime, type = "dcor") 
mic_result <- calc_correlation(full_exprs_matrix, redpath_pseudotime, type = "mic")
selected_result <- gene_selection(full_exprs_matrix, redpath_pseudotime, dcor_result, mic_result, threshold = 0.5)

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