ArrayExpressPrep: ArrayExpressnPrep

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

ArrayExpressPrep(AEaccession, var_list = NULL, rename_samples = TRUE,
  platform = NULL)

Arguments

AEaccession	An ArrayExpress accession number (i.e. 'E-MEXP-2360')
var_list	List of variables (i.e. genes) to include. If provided, data for other variables is discarded. Default: NULL
rename_samples	Replace the GEO sample name with the title
platform	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 provided in the ExpressionSet's phenoData@data$characteristics.celltype. slot. Default: TRUE

Value

A matrix of correlation values

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