diffCountsBaySeq: 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.

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.

References

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

Examples

Run this code

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)