ExprRefCompare: ExprRefCompare

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

Description

Compares the averaged expression of each cluster within a Seurat object to that of an entry in the Gene Expression Omnibus database or the ArrayExpress Archive of Functional Genomics Data

Usage

ExprRefCompare(object, ...)

## S3 method for class 'seurat'
ExprRefCompare(seuratObj, accession, GEOentry_index = 1,
  rename_samples = TRUE, do_plot = FALSE, group_by = NULL,
  add_ident = NULL, cor_function_use = cor, platform = NULL,
  probe_set = NULL, annotation_db = NULL, species = "hsapiens", ...)

## S3 method for class 'Seurat'
ExprRefCompare(object, accession, GEOentry_index = 1,
  rename_samples = TRUE, do_plot = FALSE, group_by = NULL,
  assay = "RNA", add_ident = NULL, cor_function_use = cor,
  platform = NULL, probe_set = NULL, annotation_db = NULL,
  species = "hsapiens", ...)

Arguments

object	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.
accession	A GEO or ArrayExpress accession number (i.e. 'GSE24759')
GEOentry_index	Indicate which ExpressionSet to use in a GEO entry containing multiple ExpressionSets
rename_samples	Replace the sample name with that provided in the ExpressionSet's phenoData@data slot
do_plot	Plot the correlation matrix. Default: FALSE
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
platform	For ArrayExpress datasets, the Annotation Database corresponding to the platform used in the assay (i.e. hgu133plus2.db). If not supplied, will attempt to detect the correct database and retrieve the names from Biomart (which can be SLOW) Default: NULL
probe_set	If it is difficult/impossible to find the correct annotation package for the assay, you can use biomaRt as a backup by supplying the probe_set name and species. For available probesets, run biomaRt::listAttributes(mart = useMart(mart = "ENSEMBL_MART_ENSEMBL", dataset = "species_gene_ensembl")), where species is the same as below. Default = NULL
annotation_db	For entries that do not contain a probeID-to-gene mapping, it is necessary to supply the name of the annotation package that corresponds to the assay used in the GEO/AE entry (i.e. hugene10sttranscriptcluster.db for the [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]. Default: NULL.
species	= Dataset species, in the form of genus initial, species with no space between. Default: "hsapiens"

Details

Performs a canonical correlation analysis on the two datasets and then assesses the correlation using the CCA data.

Value

A matrix of correlation values

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