constructRcadeTable: Construct Rcade Table

In jmc200/Rcade: R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data

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

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")

jmc200/Rcade documentation built on June 17, 2020, 5:59 a.m.