choose_dataset: Choose a suitable data set for Edger/DESeq

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

Choose a suitable data set for Edger/DESeq

Description

The _pairwise family of functions all demand data in specific formats. This tries to make that consistent.

Usage

choose_dataset(input, choose_for = "limma", force = FALSE, verbose = TRUE, ...)

Arguments

input	Expt input.
choose_for	One of limma, deseq, edger, or basic. Defines the requested data state.
force	Force non-standard data?
verbose	Print some information about what is happening?
...	More options for future expansion.

Details

Invoked by _pairwise().

Value

List the data, conditions, and batches in the data.

See Also

[choose_binom_dataset()] [choose_limma_dataset()] [choose_basic_dataset()]

Examples

## Not run: 
 starting_data <- create_expt(metadata)
 modified_data <- normalize_expt(starting_data, transform = "log2", norm = "quant")
 a_dataset <- choose_dataset(modified_data, choose_for = "deseq")
 ## choose_dataset should see that log2 data is inappropriate for DESeq2 and
 ## return it to a base10 state.

## End(Not run)

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