calc_correlation: Calculate correlation of gene expression with pseudotime

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

Description

This function calculates the correlation of gene expression with the inferred pseudo time.

Usage

calc_correlation(full_gene_exprs, pseudo_time, type = "dcor",
  order = F)

Arguments

full_gene_exprs	A gene (row) by cell (col) gene expression matrix with all genes.
pseudo_time	The pseudo development time / ordering of cells can be provided as input. Please leave order = F if pseudotime is provided
type	The type of correlation to calculate. "dcor" and "mic" are available (Distance correlation / Maximal Information Criterion).
order	Defaults to F. If pseudotime is provided, set to F. If an ordering of cells is provided, set to T.

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.