remove coefficient effects from counts

Source: R/remove_parameter_effects.R

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

remove_parameter_effects(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