LTMheat: Prepare the screen and sample data used for running LTMcook

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

Prepare the screen and sample data used for running LTMcook

Description

This function will separate the samples into given number of quantile groups, calculate the mantel's zstat value, nCV values of given clock gene list, gene by gene. It will output a list with screen and sample data frame used for running LTMcook.

Usage

LTMheat(
  heatD,
  benchD,
  cvGenes,
  outFileSymbol = NULL,
  outDir = NULL,
  qnum = 4,
  nCores = 1,
  releaseNote = TRUE
)

Arguments

heatD	a data frame. The first column is the gene symbol, and other columns are samples. One row per gene.
benchD	a data frame. The expression correlation values of paired clock genes.
cvGenes	a vector string. The list of clock genes representing the oscillation robustness of circadian clock.
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.
qnum	a numeric value. The number of quantile groups when separate samples based on expression level gene by gene.
nCores	an integer. Number of cores to use. For parallel computing, set nCores a integer larger than 1.
logical.	If TRUE, time used during the analysis will be released on the screen.

Value

a list with screen and sample data frame.

Examples

## please refer to the webpage of LTMR package

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