RegressOut: Regress out technical effects and cell cycle

In nukappa/seurat_v2: Seurat : R toolkit for single cell genomics

Description

Remove unwanted effects from scale.data

Usage

RegressOut(object, latent.vars, genes.regress = NULL, model.use = "linear",
  use.umi = F, do.scale = T, do.center = T, scale.max = 10)

Arguments

object	Seurat object
latent.vars	effects to regress out
genes.regress	gene to run regression for (default is all genes)
model.use	Use a linear model or generalized linear model (poisson, negative binomial) for the regression. Options are 'linear' (default), 'poisson', and 'negbinom'
use.umi	Regress on UMI count data. Default is FALSE for linear modeling, but automatically set to TRUE if model.use is 'negbinom' or 'poisson'
do.scale	Whether to scale the data.
do.center	Whether to center the data.
scale.max	Max value to accept for scaled data. The default is 10. Setting this can help reduce the effects of genes that are only expressed in a very small number of cells.

Value

Returns Seurat object with the scale.data ([e-mail]) genes returning the residuals from the regression model

nukappa/seurat_v2 documentation built on May 24, 2019, 9:57 a.m.