edge_tidiers: Tidying methods for edge's deSet object

In StoreyLab/biobroom: Turn Bioconductor objects into tidy data frames

Description

Tidying methods for edge's deSet object

Usage

## S3 method for class 'deSet'
tidy(x, addPheno = FALSE, ...)

## S3 method for class 'deSet'
augment(x, data, ...)

## S3 method for class 'deSet'
glance(x, ...)

Arguments

x	deSet object
addPheno	whether columns should be included in the tidied output for those in the ExpressionSet's phenoData
...	extra arguments (not used)
data	Original data can be added. Default is NULL.

Details

addPheno=TRUE adds columns that are redundant (since they add per-sample information to a per-sample-per-gene data frame), but that are useful for some kinds of graphs and analyses.

Value

tidy returns a data frame with one row per gene-sample combination, with columns

gene	gene name
sample	sample name (from column names)
value	expressions on log2 scale

augment returns a data.frame with

p.value	the original p-values given to qvalue
q.value	the computed q-values
lfdr	the local false discovery rate

glance returns a data.frame with the model fits

StoreyLab/biobroom documentation built on May 9, 2019, 3:09 p.m.