discoODAexclusionMatrix: Algorithm Exclusion Matrix

In DiscoRhythm: Interactive Workflow for Discovering Rhythmicity in Biological Data

Description

A small matrix indicating which algorithms should be excluded given certain experimental designs and data types.

Usage

discoODAexclusionMatrix

Format

An object of class matrix (inherits from array) with 4 rows and 7 columns.

Examples

# Code used to generate discoODAexclusionMatrix

itemNames <- c(
 "missing_value",
  "with_bio_replicate",
  "non_integer_interval",
  "uneven_interval",
  "circular_t",
  "invalidPeriod",
  "invalidJTKperiod"
)

# Creating requirements matrix, first assuming all methods are valid
# Then appying exclusion criteria of MetaCycle plus CS criteria
mat <- matrix(TRUE, nrow = 4, ncol = length(itemNames))
rownames(mat) <- c("CS", "JTK", "LS", "ARS")
colnames(mat) <- itemNames

# Exclusion criteria from MetaCycle v1.1, i.e. can algorithm handle XXX
mat[c("ARS", "JTK"), c("non_integer_interval", "uneven_interval")] <- FALSE
mat["ARS", "with_bio_replicate"] <- FALSE
mat["ARS", "missing_value"] <- FALSE
mat["JTK", "invalidJTKperiod"] <- FALSE

# Additional exclusion criteria
mat["ARS", "circular_t"] <- FALSE
mat[c("CS", "JTK", "ARS", "LS"), "invalidPeriod"] <- FALSE

discoODAexclusionMatrix <- mat

DiscoRhythm documentation built on Nov. 8, 2020, 7:32 p.m.