driving_force_gene_selection: A feature/ gene selection function
In uSORT: uSORT: A self-refining ordering pipeline for gene selection

Description Usage Arguments Value Author(s) Examples

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

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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)

`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.

integer

MaiChan Lau

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)