A feature/ gene selection function

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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

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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

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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)

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