diffCountsBaySeq {Rcade} | R Documentation |
Most Rcade users will not need to call this function directly. A function that provides a wrapper for the methods in the BaySeq package.
diffCountsBaySeq(counts, targets, annoZones, cl = NULL, getLibsizesArgs = list(estimationType = "quantile", quantile = 0.75), getPriors.NBArgs = list(), getLikelihoods.NBArgs = list(), libsizes)
counts |
Counts from |
targets |
|
annoZones |
|
cl |
|
getLibsizesArgs |
See |
getPriors.NBArgs |
See
|
getLikelihoods.NBArgs |
See
|
libsizes |
Library sizes FIXME |
data.frame
containing differential count information.
Jonathan Cairns
Hardcastle, T. J., & Kelly, K. A. (2010). baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics, 11, 422.
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)