CP_Rhythmicity: Title The Rhythmicity Analysis with Cosinor

In XiangningXue/CircadianPipeline: What the Package Does (One Line, Title Case)

Title The Rhythmicity Analysis with Cosinor

Description

This function either takes one data set and performs only rhythmicity analysis with cosinor, or takes two data sets and categorize the genes into joint rhythmicity categories.

Usage

CP_Rhythmicity(
  x1,
  x2 = NULL,
  method = "Sidak_FS",
  period = 24,
  alpha = 0.05,
  alpha.FDR = 0.05,
  CI = FALSE,
  p.adjust.method = "BH",
  parallel.ncores = 1
)

Arguments

x1	group I data. A list with the following components: data: data.frame genes in rows and samples in columns. time: time of expression. Should be in the same order as samples in the data. gname: labels for gene. Should be in the same order as rows in the data.
x2	group II data. Same as x1 for formats.
method	character string specifying the algorithm used for joint rhythmicity categorization. Should be one of "Sidak_FS", "Sidak_BS", "VDA", "AWFisher".
period	integer. The length of the oscillation cycle. Default is 24 for circadian signals.
alpha	integer. Threshold for rhythmicity p-value in joint rhythmicity categorization. If CI = TRUE, (1-alpha) confidence interval for parameters will be returned.
alpha.FDR	integer. Threshold for rhythmicity p-value in joint rhythmicity categorization adjusted for global FDR control.
CI	logical. Should confidence interval for A, phase and M be returned?
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 list of origical x input and rhythmicity analysis estimates. If given two data sets, joint rhythmicity categorization will also be available in component rhythm.joint

Examples

x = CP_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 = CP_Rhythmicity(x1 = x[[1]], x2 = x[[2]])

XiangningXue/CircadianPipeline documentation built on May 3, 2022, 3:04 p.m.