LTMcut: Prepare the input data for a quick run of LTMheat

In gangwug/LTMR: An in silico genome-wide screen for circadian clock strength

Prepare the input data for a quick run of LTMheat

Description

This function will select genes with high expression values and large expression variations across samples for a quick run of LTMheat.

Usage

LTMcut(
  cutD = NULL,
  exemptGenes = NULL,
  minExp = -1e+10,
  minFold = 1,
  outFileSymbol = NULL,
  outDir = NULL
)

Arguments

cutD	a data frame. The first column is the gene symbol, and other columns are samples. One row per gene.
exemptGenes	a character vector. A list of clock genes that will be kept in the output data frame without getting into the filtration process.
minExp	a numeric value. The minimal median expression value in quantile group 1.
minFold	a numeric value. The minimal fold change between quantile group 4 and quantile group 1. Median value in each quantile group is used.
outFileSymbol	a character string. A prefix exists in the name of output file. Set it NULL(default) if prefer to return a data frame.
outDir	a character string. The name of directory used to store output file.

Value

a data fame prepared for a quick run of LTM

Examples

## please refer to the webpage of LTMR package

gangwug/LTMR documentation built on Dec. 30, 2022, 10:43 p.m.