deseq_try_sv: Given a set of surrogate variables from sva and friends, try...

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

Given a set of surrogate variables from sva and friends, try adding them to a DESeqDataSet.

Description

Sometimes sva returns a set of surrogate variable estimates which lead to models which are invalid according to DESeq2. This function will try before buying and tell the user if the sva model additions are valid according to DESeq.

Usage

deseq_try_sv(data, summarized, svs, num_sv = NULL)

Arguments

data	DESeqDataSet to test out.
summarized	Existing DESeq metadata to append svs.
svs	Surrogates from sva and friends to test out.
num_sv	Optionally, provide the number of SVs, primarily used if recursing in the hunt for a valid number of surrogates.

Value

DESeqDataSet with at least some of the SVs appended to the model.

See Also

[sva] [RUVSeq] [all_adjusters()] [normalize_batch()]

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