remove some effects from the counts

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 (recall a brentlabRnaSeqSet is a child, so that works, too)

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