DCP_DiffR2: Differential Rhythmicity Fitness Test

In DiffCircaPipeline/Rpackage: An R package for DiffCircaPipeline: A framework for multifaceted characterization of differential rhythmicity

Differential Rhythmicity Fitness Test

Description

Differential Rhythmicity Fitness Test

Usage

DCP_DiffR2(
  x,
  method = "LR",
  TOJR = NULL,
  alpha = 0.05,
  nSampling = 1000,
  Sampling.save = NULL,
  Sampling.file.label = "gII_vs_gI",
  p.adjust.method = "BH",
  parallel.ncores = 1
)

Arguments

x	outpuf of DCP_Rhythmicity(x1, x2)
method	one of "LR", "permutation", "bootstrap". "LR" is recommended.
TOJR	toTOJR output. If NULL, rhythm.joint object in x will be used.
alpha	cutoff of p-values for significant differential rhythm fitness change.
nSampling	number of samplings if "permutation" or "bootstrap" is chosen for method
Sampling.save	directory to save sampling results. If NULL, the result will not be saved.
Sampling.file.label	character string. Used as file lable if sampling results are saved.
p.adjust.method	input for p.adjust() in R package stat
parallel.ncores	integer. Number of cores used if using parallel computing with mclapply(). Not functional for windows system.

Value

A dataframe of differential rhythm finess test results.

Examples

x = DCP_sim_data(ngene=1000, nsample=30, A1=c(1, 3), A2=c(1, 3),
phase1=c(0, pi/4), phase2=c(pi/4, pi/2),
M1=c(4, 6), M2=c(4, 6), sigma1=1, sigma2=1)
rhythm.res = DCP_Rhythmicity(x1 = x[[1]], x2 = x[[2]])
rhythm.diffR2 = DCP_DiffPar(rhythm.res)

DiffCircaPipeline/Rpackage documentation built on March 17, 2023, 7:32 a.m.