diffCountsBaySeq {Rcade} | R Documentation

## Differential Counts wrapper - BaySeq

### Description

Most Rcade users will not need to call this function directly. A function that provides a wrapper for the methods in the BaySeq package.

### Usage

    diffCountsBaySeq(counts, targets, annoZones, cl = NULL, getLibsizesArgs = list(estimationType = "quantile", quantile = 0.75), getPriors.NBArgs = list(), getLikelihoods.NBArgs = list(), libsizes)

### Arguments

`counts` | Counts from `countReads`
`targets` | `Data.frame` - Information about the ChIP data files. Mandatory column names are: "fileid", "sampleid", "factor", "filepath".
`annoZones` | `GRanges` specifying the bins of interest, with a column in the metadata for the geneID.
`cl` | `cluster` from `makeCluster` in the parallel package.
`getLibsizesArgs` | `List` - Arguments to be passed to the getLibsizes function. If a `libsizes` column is present in the targets file, then these arguments are ignored. `getLibsizesArgs$cD` is always ignored. See `getLibsizes` for a list of arguments.
`getPriors.NBArgs` | See `getPriors` for a list of arguments. `getPriors.NBArgs$cD` and `getPriors.NBArgs$cl` are always ignored.
`getLikelihoods.NBArgs` | See `getLikelihoods` for a list of arguments. `getLikelihoods.NBArgs$cD` and `getLikelihoods.NBArgs$cl` are always ignored.
`libsizes` | Library sizes FIXME

### Value

`data.frame` containing differential count information.

### Author(s)

Jonathan Cairns

### References

Hardcastle, T. J., & Kelly, K. A. (2010). baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics, 11, 422.

### See Also

`RcadeAnalysis`

### Examples

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

    	targets <- read.csv(file.path(dir, "targets.csv"), as.is = TRUE)

    	anno <- read.csv(file.path(dir, "anno.csv"))
    	anno <- anno[order(anno$chromosome_name),]
    	colnames(anno) <- c("ENSG","chr","start","end","str")
    	ChIPannoZones <- defineBins(anno, zone=c(-1500, 1500), geneID="ENSG")

    	counts <- countReads(ChIPannoZones, targets, fileDir = dir)

    	x <- diffCountsBaySeq(counts, targets, ChIPannoZones)

[Package Rcade version 1.24.0 Index]