RegressRegNB: Use regularized negative binomial regression to normalize UMI...

In atakanekiz/Seurat3.0: Tools for Single Cell Genomics

Description

This function calls sctransform::vst. The sctransform package is available at https://github.com/ChristophH/sctransform. Use this function as an alternative to the NormalizeData, FindVariableFeatures, ScaleData workflow. Results are saved in the assay's data and scale.data slot, and sctransform::vst intermediate results are saved in misc slot of seurat object.

Usage

RegressRegNB(object, assay = NULL, do.correct.umi = FALSE,
  variable.features.rv.th = 1.3, variable.features.n = NULL,
  return.dev.residuals = FALSE, clip.range = c(-10, 10),
  do.scale = FALSE, do.center = TRUE, verbose = TRUE, ...)

Arguments

object	A seurat object
assay	Name of assay to use
do.correct.umi	Place corrected UMI matrix in assay data slot
variable.features.rv.th	Features with residual variance greater or equal this value will be selected as variable features; default is 1.3
variable.features.n	Use this many features as variable features after ranking by residual variance
return.dev.residuals	Place deviance residuals instead of Pearson residuals in scale.data slot; default is FALSE
clip.range	Range to clip the residuals to; default is c(-10, 10)
do.scale	Whether to scale residuals to have unit variance; default is FALSE
do.center	Whether to center residuals to have mean zero; default is TRUE
verbose	Whether to print messages and progress bars
...	Additional parameters passed to sctransform::vst

atakanekiz/Seurat3.0 documentation built on May 26, 2019, 2:33 a.m.