README.md

In AHallLab/triad.expression: Analysis of gene expresson for wheat genome triads.

triad.expression

Description

The triad.expression R package seeks to provide methods for analyzing and visualizing information such as gene expression balance in sets of homologous genes in the Wheat genome called Triads.

A Triad is a set of three homologous (related in position and function) genes where a gene exists in the A, B, and D sub genomes of Wheat.

Each of the three genes in a triad may be expressed at different levels in different tissues or in different Wheat varieties. This is sometimes referred to as "Triad Balance".

triad.expression allows you to compute mean gene expression levels of triads across combinations of factors such as experimental condition, or tissue, allowing the detection of changes in gene expression between levels of those factors. From such data "Triad Balance" can then be computed, and visualized using ternary plots or loom plots.

Features Summary

• Example data sets
• Compute mean gene expression across factors
• Calculate and assign "Triad Balance"
• Visualize Triad data across chromosomes with "Loom Plots"
• Visualize Triad Balance of all triads with ternary plots

Installation

triad.expression is not currently published on CRAN, so you will have to install triad.expression yourself from this GitHub repository. But that's ok, it's easy enough.

The easiest way to do this is to use the install_github command from the R devtools package like so:

devtools::install_github()

If you do not have devtools installed, no problem, that is available through CRAN and so using

install.packages("devtools") 

in an R session should install it for you.

Once installed, use the package with library.

library(triad.expression)
library(dplyr) # dplyr is going to be useful too.

AHallLab/triad.expression documentation built on Dec. 17, 2021, 6:41 a.m.