driving_force_gene_selection: A feature/ gene selection function

In JinmiaoChenLab/uSORT: uSORT: A self-refining ordering pipeline for gene selection

Description

A feature/ gene selection function (1) removes sparsely expressed genes, (2) identifies differentially expressed genes based on preliminary cell ordering, (3) removes highly dispersed genes from the identified DEGs, (4) further picks genes which are expected to have large expression difference on the 2 extreme ends of preliminary cell ordering

Usage

driving_force_gene_selection(cds, scattering.cutoff.prob = 0.75,
  driving.force.cutoff = NULL, qval_cutoff = 0.05, min_expr = 0.1,
  data_type = c("linear", "cyclical"), nCores = 1)

Arguments

cds	a Monocle's CellDataSet object
scattering.cutoff.prob	probability used for removing largely dispersed genes
driving.force.cutoff	a value used for removing genes which do not change much along cell progress along cell progress path
qval_cutoff	a user-defined adjusted p-value below which genes are retained
min_expr	the minimum expression value
data_type	a character indicating the type of underlying cell progression, i.e. linear or cyclical.
nCores	Number of cores to use.

Value

integer

Author(s)

MaiChan Lau

Examples

dir <- system.file('extdata', package='uSORT')
file <- list.files(dir, pattern='.txt$', full=TRUE)
#exprs <- uSORT_preProcess(exprs_file = file)
#exp_raw <- t(exprs$exprs_raw)
#exp_trimmed <- t(exprs$exprs_log_trimed)
#cds <- uSORT:::EXP_to_CellDataSet(exp_trimmed, exp_raw)
#driver_genes <- driving_force_gene_selection(cds = cds)

JinmiaoChenLab/uSORT documentation built on May 7, 2019, 10:53 a.m.