removeParameterEffects: remove some effects from the counts

In cmatKhan/brentlabRnaSeqTools: A Collection of Functions to Interact with the Brentlab RNASeq Database

Description

subtract effect from norm counts of a single factor from coef x design. coef is in normalized log space. dds must have been created with model.matrix

Usage

removeParameterEffects(deseq_object, col_indicies)

Arguments

deseq_object	a deseq data object REQUIRED: the object must have been created with a model.matrix rather than a formula for the design argument
col_indicies	a numeric vector corresponding to the column indicies of the batch parameters you'd like to remove

Value

a log2 scale gene by samples matrix with desired effects removed

Note

works for both formula and model.matrix designs in the dds object

cmatKhan/brentlabRnaSeqTools documentation built on Nov. 17, 2021, 5:47 a.m.