libScales: Generates library scaling factors from ribosome footprint...

In riboSeqR: Analysis of sequencing data from ribosome profiling experiments

Description

This function applies the library scaling factor estimation methods implemented in the baySeq package to ribosome footprint data and (if present) the associated RNA-Seq data. The library scaling factors can then be used in downstream analyses.

Usage

libScales(rC, riboDat, lengths, frames, method = "edgeR")

Arguments

rC	A riboCoding object containing the coordinates of the coding sequences and the number of ribosomal footprint reads of various classes to be found in each.
riboDat	A riboData object containing the ribosome footprint and RNA-seq alignments.
lengths	Lengths of ribosome footprints to inform count data.
frames	Frames of ribosome footprints (relative to coding start site). If omitted, all frames are used.
method	Method to be used for scaling factor estimation. See getLibsizes

Value

A list object containing

riboLS	Ribosome footprint library scaling factors.
rnaLS	RNA-Seq library scaling factors.

Author(s)

Thomas J. Hardcastle

riboSeqR documentation built on Nov. 8, 2020, 8:23 p.m.