Rcade (version 1.14.0)

constructRcadeTable: Construct Rcade Table

Description

Most Rcade users will not need to call this function directly. This function constructs a full Rcade table from ChIP and DE data.

Usage

constructRcadeTable(DE, DElookup, chip, annoZone, annoZoneGeneidName, DE.prior=NULL, ChIP.prior=NULL, prior.mode, prior=NULL)

Arguments

DE

data.frame - DE data (see details section, below)

DElookup

list - a lookup table specifing the columns of interest in the DE argument. FIXME - list mandatory columns

chip

data.frame - ChIP information as ... Columns correspond to samples, and rows should correspond to bins defined by the annoZone arguments's rows.

annoZone

GRanges - The genomic bins used in the ChIP-seq analysis. FIXME Metadata must be present.

annoZoneGeneidName

character - The column in the metadata of annoZone argument that contains the geneIDs.

DE.prior

As per RcadeAnalysis

ChIP.prior

As per RcadeAnalysis

prior.mode

As per RcadeAnalysis

prior

As per RcadeAnalysis

Value

data.frame

See Also

RcadeAnalysis

Examples

	data(RcadeSTAT1)

	dir <- file.path(system.file("extdata", package="Rcade"), "STAT1")

	DE <- getDE(RcadeSTAT1)
	DElookup <- list(GeneID="ENSG", logFC="logFC", B="B",
		"Genes.Location", "Symbol")

	chip <- getChIP(RcadeSTAT1)
	annoZone <- getChIP(RcadeSTAT1, what="annoZones")

	x <- constructRcadeTable(DE, DElookup, chip, annoZone, annoZoneGeneidName="ENSG", prior.mode="assumeIndependent")