rnaseq_ic {biotmle}R Documentation

Transformation utility for using "voom" with biomarker TMLE procedure

Description

This function prepares next-generation sequencing data (counts) for use with the biomarker TMLE procedure by invoking the voom transform of limma.

Usage

rnaseq_ic(biotmle, weights = TRUE, ...)

Arguments

biotmle

(bioTMLE) - subclass of SummarizedExperiment containing next-generation sequencing (NGS) count data in the "assays" slot.

weights

(logical) - whether to return quality weights of samples in the output object.

...

- other arguments to be passed to functions limma::voom or limma::voomWithQualityWeights as appropriate.

Value

EList object containing voom-transformed "expression" measures of count data (actually, the mean-variance trend) in the "E" slot, to be passed into the biomarker TMLE procedure.


[Package biotmle version 1.10.0 Index]