expt: An expt is an ExpressionSet superclass with a shorter name.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

An expt is an ExpressionSet superclass with a shorter name.

Description

It is also a simple list so that one may summarize it more simply, provides colors and some slots to make one's life easier. It is created via the function create_expt() which perhaps should be changed.

Usage

expt(...)

Arguments

...	Parameters for create_expt()

Details

Another important caveat: expressionSets and their methods are all S4; but I did not want to write S4 methods, so I made my expt a S3 class. As a result, in order to make use of exprs, notes, pData, fData, and friends, I made use of setMethod() to set up calls for the expressionSet portion of the expt objects.

Slots

title

Title for the expressionSet.

notes

Notes for the expressionSet (redundant with S4 notes()).

design

Copy of the experimental metadata (redundant with pData()).

annotation

Gene annotations (redundant with fData()).

gff_file

filename of a gff file which feeds this data.

state

What is the state of the data vis a vis normalization, conversion, etc.

conditions

Usually the condition column from pData.

batches

Usually the batch column from pData.

libsize

Library sizes of the data in its current state.

colors

Chosen colors for plotting the data.

tximport

Data provided by tximport() to create the exprs() data.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.