RelaRate.test: Relative Rate Test for Gene Expression

In jingwyang/TreeExp: the R package for analyzing expression evolution based on RNA-seq data

Description

statistically compare the relative expression rate of a given set of genes between two taxa (or species)

Usage

RelaRate.test(expTable = NULL, x = NULL, y = NULL, outgroup = NULL,
  Pi = 0, alternative = c("two.sided", "less", "greater"))

Arguments

expTable	an exprssion level table: column corresponds to median expression value of all biological samples within one taxa_subtaxa group; row corresponds to othologous genes
x	taxa name
y	taxa name
outgroup	outgroup name
Pi	value of parameter Pi which measures the variance of optima among genes under sOU model. Pi = 0 by default.
alternative	character string specifying the alternative hypothesis, must be one of "two.sided" (default), "greater" or "less".

Value

A list containing the following components:

• Z_score the z-statistic

• alternative records the value of the input argument alternative: "greater", "less" or "two.sided".

• p.value the p-value for the test

Author(s)

Jingwen Yang

Examples

data(tetraExp)
exp_table <-exptabTE(tetraExp, taxa = 'all', subtaxa = 'Brain',rowindex = 1:100)
ztest <- RelaRate.test(expTable = exp_table, x = 'human', y = 'chimpanzee',
outgroup = 'macaque', alternative = 'greater')
ztest

jingwyang/TreeExp documentation built on June 11, 2019, 6:17 p.m.