vstExprs: Return a variance-stabilized matrix of expression values

Description Usage Arguments

View source: R/expr_models.R

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

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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. 20, 2017, 2:02 a.m.