tidy.deSet: Tidying methods for edge's deSet object
Description
Tidying methods for edge's deSet object
Usage
"tidy"(x, addPheno = FALSE, ...)
"augment"(x, data, ...)
"glance"(x, ...)
Arguments
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.
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
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.