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

### 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")

[Package Rcade version 1.28.0 Index]