segmentSeq (version 2.6.0)

segmentSeq-package: Segmentation of the genome based on multiple samples of high-throughput sequencing data.

Description

The segmentSeq package is intended to take multiple samples of high-throughput data (together with replicate information) and identify regions of the genome which have a (reproducibly) high density of tags aligning to them. The package was developed for use in identifying small RNA precursors from small RNA sequencing data, but may also be useful in some mRNA-Seq and chIP-Seq applications.

Details

Package:

segmentSeq

Type:

Package

Version:

0.0.2

Date:

2010-01-20

License:

GPL-3

LazyLoad:

yes

Depends:

baySeq, ShortRead

To use the package, we construct an alignmentData object from sets of alignment files using either the readGeneric function to read text files or the readBAM function to read from BAM format files.

We then use the processAD function to identify all potential subsegments of the data and the number of tags that align to these subsegments. We then use either a heuristic or empirical Bayesian approach to segment the genome into `loci' and `null' regions. We can then acquire posterior likelihoods for each set of replicates which tell us whether a region is likely to be a locus or a null in that replicate group.

The segmentation is designed to be usable by the baySeq package to allow differential expression analyses to be carried out on the discovered loci.

The package (optionally) makes use of the 'snow' package for parallelisation of computationally intensive functions. This is highly recommended for large data sets.

See the vignette for more details.

References

Hardcastle T.J., Kelly, K.A. and Balcombe D.C. (2011). Identifying small RNA loci from high-throughput sequencing data. In press.

See Also

baySeq

Examples

# Define the chromosome lengths for the genome of interest.

chrlens <- c(2e6, 1e6)

# Define the files containing sample information.

datadir <- system.file("extdata", package = "segmentSeq")
libfiles <- c("SL9.txt", "SL10.txt", "SL26.txt", "SL32.txt")

# Establish the library names and replicate structure.

libnames <- c("SL9", "SL10", "SL26", "SL32")
replicates <- c(1,1,2,2)

# Process the files to produce an 'alignmentData' object.

alignData <- readGeneric(file = libfiles, dir = datadir, replicates =
replicates, libnames = libnames, chrs = c(">Chr1", ">Chr2"), chrlens =
chrlens)

# Process the alignmentData object to produce a 'segData' object.

sD <- processAD(alignData, gap = 100, cl = NULL)