vst_advice: Advise how VST will transform data

In MonashBioinformaticsPlatform/varistran: Variance Stabilizing Transformations appropriate for RNA-Seq expression data

Description

Advise how VST will transform data

Usage

vst_advice(
  what = "anscombe.nb",
  dispersion = NULL,
  cpm = FALSE,
  lib.size = NULL
)

Arguments

what	Either the output of a call to vst() or the name of a VST method (see vst() help).
dispersion	As per vst().
cpm	As per vst().
lib.size	As per vst().

Value

A data frame giving an indication of how an average sample will be transformed.

The column "twofold_step" shows the step from the previous to current row. With a log2 transformation this would be uniformly 1, but with a VST and small counts the step is less than 1. This therefore provides advice on how compacted the VST is near zero-count, as compared to a log2 transformation.

Note that the results given are for an average sample. Where library sizes differ wildly, the VST may perform poorly.

MonashBioinformaticsPlatform/varistran documentation built on March 21, 2020, 3:20 p.m.