full_mode_analysis: full_mode_analysis

In AndreaRP/CircaN: Identification Of Circadian Patterns In Omics Data

Description

Runs analysis on CircaN, JTK and MetaCycle and integrates the results.

Usage

full_mode_analysis(
  data,
  s2c,
  algorithms = c("circan", "jtk", "metacycle"),
  min_per = 20,
  max_per = 28,
  circan_init_value = 24,
  circan_mode = "port",
  mc_cycMethod = c("LS", "JTK")
)

Arguments

data	The data matrix with the omics data.
s2c	Data frame with at least the columns sample (which must coincide with the samples in data) and time (recording time corresponding to each sample.
algorithms	character vector indicating which algorithms to test the data with. Must beone, or a combination of circan, jtk and metacycle.
min_per	Minimum period to search for.
max_per	Maximum period to search for.
circan_init_value	Initial value for the period of CircaN regression.
circan_mode	Algorithm to use in CircaN regression. Must be one of 'default' for Gauss-Newton, 'plinear' for the Golub-Pereyra algorithm for partially linear least-squares models and 'port' for the ‘nl2sol’ algorithm from the Port library.
mc_cycMethod	a character vector(length 1 or 2 or 3) for MetaCycle. User-defined methods for detecting rhythmic signals, must be selected as any one, any two or all three methods(default) from "ARS"(ARSER), "JTK"(JTK_CYCLE) and "LS"(Lomb-Scargle).

Examples

results <- full_mode_analysis(my_data, s2c)

AndreaRP/CircaN documentation built on Jan. 25, 2021, 5:49 a.m.