R: Construct Rcade Table

constructRcadeTable {Rcade}

R Documentation

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

Author(s)

Jonathan Cairns

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")

[Package Rcade version 1.29.0 Index]