Class "alignmentData"

Description

The alignmentData class inherits from the alignmentClass class and records information about a set of alignments of high-throughput sequencing data to a genome. Details include the alignments themselves, the chromosomes of the genome to which the data are aligned, and counts of the aligned tags from each of the libraries from which the data come.

Objects from the class

Objects can be created by calls of the form new("alignmentData", ...), but more usually by using one of readBAM or readGeneric functions to generate the object from a set of alignment files.

Slots

alignments:

Object of class "GRanges". Stores information about the alignments. See Details.

replicates:

Object of class "factor". Replicate information for each of the libraries. See Details.

data:

Object of class "matrix". For each alignment described in the alignments slot, contains the number of times the alignment is seen in each sample.

libnames:

Object of class "character". The names of the libraries for which alignment data exists.

libsizes:

Object of class "numeric". The library sizes (see Details) for each of the libraries.

Details

The alignments slot is the key element of this class. This is a GRanges object that, in addition to the usual elements defining the location of aligned objects to a reference genome, also describes the values ‘tag’, giving the sequence of the tag aligning to the location, ‘matches’, indicating in how many places that tag matches to the genome, ‘chunk’, an identifier for the sets of tags that align close enough together to form a potential locus, and ‘chunkDup’, indicating whether that tag matches to multiple places within the chunk.

The library sizes, defined in the libsizes slot, provide some scaling factor for the observed number of counts of a tag in different samples.

The replicates slot is a vector of factors such that the ith sample is a replicate of the jth sample if and only if @replicates[i] == @replicates[j].

Methods

[

signature(x = "alignmentData"): ...

dim

signature(x = "alignmentData"): ...

initialize

signature(.Object = "alignmentData"): ...

show

signature(object = "alignmentData"): ...

Author(s)

Thomas J. Hardcastle

See Also

alignmentClass, the class from which 'alignmentData' inherits. readGeneric, which will produce a 'alignmentData' object from appropriately formatted tab-delimited files. readBAM, which will produce a 'alignmentData' object from BAM files. processAD, which will convert an 'alignmentData' object into a 'segData' object for segmentation.

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)

Results

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> library(segmentSeq)
Loading required package: baySeq
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: abind
Loading required package: perm
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/segmentSeq/alignmentData-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: alignmentData-class
> ### Title: Class "alignmentData"
> ### Aliases: alignmentData-class alignmentData [,alignmentData-method
> ###   [,alignmentData,ANY,ANY-method [,alignmentData,ANY-method
> ###   dim,alignmentData-method initialize,alignmentData-method
> ###   show,alignmentData-method cbind,alignmentData-method
> ### Keywords: classes
> 
> ### ** 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)
Reading files........done!
Analysing tags...........done!
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>