testHourglassModel: Test the hypothesis of the developmental hourglass by...

In asishallab/GeneFamilies: Analyses different properties of gene families

Test the hypothesis of the developmental hourglass by carrying out various t-tests. In these, compare the distributions of expression profile distances within a given tissue between gene classes. This should show which gene class contributes to the hourglass model. Also compare for a given gene class early and late developmental tissues with intermediate samples. This should show wether early and late stages are more diverse than intermediate ones, and thus give the hourglass shape.

Description

Test the hypothesis of the developmental hourglass by carrying out various t-tests. In these, compare the distributions of expression profile distances within a given tissue between gene classes. This should show which gene class contributes to the hourglass model. Also compare for a given gene class early and late developmental tissues with intermediate samples. This should show wether early and late stages are more diverse than intermediate ones, and thus give the hourglass shape.

Usage

testHourglassModel(x, tissues = c("seedling", "cotyledon",
  "developing leaf", "flower stage 9", "flower stage 16"),
  gene.classes = c("Orthologs", "Non-Orthologs"),
  early.late.indx = c(2, 4), intermediate.indx = 3,
  statistic = "median")

Arguments

x	an instance of base::data.frame with columns: 'Family', 'Statistic', 'Gene.Class', 'Value', 'Tissue'. For example this package's data tandems.exp.prof.dists.tissue.orth.dist.
tissues	a character vector identifying the tissues to be investigated. Default is c('seedling', 'cotyledon', 'developing leaf', 'flower stage 9', 'flower stage 16').
gene.classes	a character vector identifying the gene classes to be investigated. Default is c('Orthologs', 'Non-Orthologs').
early.late.indx	A numeric vector identifying which entries of tissues are considered early and late developmental stages. Default is c(2,4).
intermediate.indx	A single integer identifying which entry in tissues is considered to be the intermediate developmental stage. Default is 3.
statistic	a string identifying which statistic of x to be investigated. Default is 'median'.

Value

A base::data.frame with columns: 'Tissue', 'Alternative.Hypothesis', 'p.value', 'effect.size', 'p.value.adjusted'

asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.