SeuratCompareR: SeuratCompareR

In milescsmith/exprcompareR: Performs correlation analysis of Seurat data and a Gene Expression Omnibus or ArrayExpress Archive of Functional Genomics Data entry

Description

Uses Canonical Correlation Analysis to compare the expression profile of the identity classes of a Seurat object to those of a second Seurat object

Usage

SeuratCompareR(first.obj, ...)

## S3 method for class 'seurat'
SeuratCompareR(first.obj, second.obj, group.by = NULL,
  add.ident = NULL, cor.function.use = cor, do.plot = FALSE, ...)

## S3 method for class 'Seurat'
SeuratCompareR(first.obj, second.obj, group.by = NULL,
  add.ident = NULL, cor.function.use = cor, do.plot = FALSE, ...)

Arguments

first.obj	Either a processed Seurat object (with ScaleData run) or the output from AverageExpression. If a Seurat object is passed, AverageExpression will be run.
...	Additional parameters to pass to the correlation function.
second.obj	A second (or the same) processed Seurat object or the output from AverageExpression for such an object.
group.by	Identifier or meta.data column by which to group the data. Default: 'ident'
add.ident	An additional identifier to use as a grouping variable. Default: NULL
cor.function.use	Function to use to calculate correlation. Default: stats::cor
do.plot	Plot the correlation matrix. Default: FALSE)

Value

A matrix of correlation values

milescsmith/exprcompareR documentation built on July 26, 2019, 4:59 a.m.