GEOprep: GEOprep

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

Description

Processes an entry in the Gene Expression Omnibus database for use in GEOcompare

Usage

GEOprep(GEOaccession, var_list = NULL, index = 1, probe_set = NULL,
  annotation_db = NULL, species = "hsapiens", rename_samples = TRUE)

Arguments

GEOaccession	A GEO accession number (i.e. 'GSE24759')
index	Indicate which ExpressionSet to use in a GEO entry containing multiple ExpressionSets. Default: 1
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" .
rename_samples	Replace the GEO sample name with the title provided in the ExpressionSet's phenoData@data slot. Default: TRUE
var.list	List of variables (i.e. genes) to include. If provided, data for other variables is discarded. Default: NULL

Value

A matrix of correlation values

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