Seurat (version 1.4.0)

RegressOut: Regress out technical effects and cell cycle

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