redpath: redPATH 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 performs the redPATH algorithm for single cell gene expression data, obtaining the pseudo development time of each single cell.

Usage

redpath(cell_gene_exprs, threadnum, step_size = 1,
  base_path_range = c(3:7), dist_type = "KL2", clustMethod = "Corr")

Arguments

cell_gene_exprs	The gene expression input obtained from get_GO_exp
threadnum	The number of threads to use
step_size	The interval of paths to merge in the final solution. Defaults to 1.
base_path_range	Sets the range of any consequtive 5 cluster solutions to calculate the base path. The maximum number can be 10 (ie c(6:10)). Defaults to c(3:7).
clustMethod	= "Corr" This sets the clustering method used. Defaults to "Corr", which is hierarchical clustering on doubly centered matrix. "GMM" is also available for Gaussian Mixture Model.

Examples

redpath_pseudotime <- redpath(data, threadnum = 4) 

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