CombiFilter: CombiFilter

In nathansam/CircadianTools: Collection of Tools for Detecting Rhythmic Genes

Description

Filters a transcriptomics dataset by using ZeroFilter, AnovaFilter and SizeFilter.

Usage

CombiFilter(
  dataset,
  non_zero_num = 4,
  threshold = 0.05,
  cutoff = 0.1,
  anovafilter = TRUE,
  zerofilter = TRUE,
  sizefilter = TRUE,
  nthreads = NULL
)

Arguments

dataset	A transcriptomics dataset. First columns should be gene names. All other columns should be expression levels.
non_zero_num	The minimum number of non-zero activity readings for genes in the filtered dataset.
threshold	Set the p-value threshold for the filtering.
cutoff	Proportion of total number of genes (which show at least some activity) to be removed.
anovafilter	Logical. If anovafiltering should be used. Defaults to TRUE.
zerofilter	Logical. If zero filtering should be used. Defaults to TRUE.
sizefilter	Logical. If size filtering should be used. Defaults to TRUE.
nthreads	Number of processor threads for the filtering. If not specified then the maximum number of logical cores are used.

Examples

Laurasmappings.filtered <- CombiFilter(Laurasmappings, nthreads = 2)

nathansam/CircadianTools documentation built on Dec. 26, 2019, 11:30 a.m.