Random-Background-distributions-of-Traits: Generate a background distibution of composite Z scores
In Jorisvansteenbrugge/TcT: Trait-based Comparative Transcriptomics

Random Background distributions of Traits

R Documentation

Generate a background distibution of composite Z scores

Description

Create a random background distribution of distances between genes in a random trait. When multiple distance metrics are provided, a composite Z score is calculated. The background distribution is determined by first random sampling two genomes. Between the two genomes the overlap in annotations is determined. Based on the overlap a trait is artificially created containing N annotations. For each annotation in the trait, the distances are calculated between Genome A and Genome B, as described in the previous section

Usage

Random_Trait_Background(
  RNAseq.data,
  bkgd.individual.Zscores,
  N,
  metrics,
  Z,
  threads = 4
)

Arguments

`RNAseq.data`	Collection of multple components, include RNA seq data, annotations, etc. See `Pre_process_input` for the full list.
`N`	Number of genes to include in the random module
`metrics`	Named list containing possibly multiple functions for distance
`Z`	Number of iterations, if left empty the actual sizes of the modules in the database will be used.
`threads`	Number of cpu cores to be used