vstExprs: Return a variance-stabilized matrix of expression values

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

This function was taken from the DESeq package (Anders and Huber) and modified to suit Monocle's needs. It accpets a either a CellDataSet or the expression values of one and returns a variance-stabilized matrix based off of them.

Usage

vstExprs(cds, dispModelName = "blind", expr_matrix = NULL,
  round_vals = TRUE)

Arguments

cds	A CellDataSet to use for variance stabilization.
dispModelName	The name of the dispersion function to use for VST.
expr_matrix	An matrix of values to transform. Must be normalized (e.g. by size factors) already. This function doesn't do this for you.
round_vals	Whether to round expression values to the nearest integer before applying the transformation.

monocle documentation built on Nov. 8, 2020, 5:06 p.m.