MapperSet-class: Class to Contain GS Reference Mapper Output

In R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

Description

Container to store data imported from a project of Roche's GS Reference Mapper Software. It stores all information into a Biobase ExpressionSet.

Objects from the Class

Objects can be created by calls of the form MapperSet(filename). While filename is a vector containing all sample directories (i.e. directories that contain the files "mapping/454HCDiffs.txt" and "mapping/454NewblerMetrics.txt").

Slots

assayData:

Object of class AssayData. Contains the number of reads with the respective difference and the total coverage for every variant in forward and reverse direction.

featureData:

Object of class AnnotatedDataFrame. Contains information about the type, location and reference of each variant. If available, it shows further Ensembl variant-ids for known SNPs.

phenoData:

Object of class AnnotatedDataFrame. By default, the phenoData contains the accession number of every sample.

variantFilterPerc:

Object of class numeric. Contains a threshold to display only those variants, whose coverage (in percent) in forward and reverse direction in at least one sample is higher than this filter value. See setVariantFilter for details about setting this value.

variantFilter:

Object of class character. Contains a vector of variant names whose coverage (in percent) in forward and reverse direction in at least one sample is higher than the filter value(s) in variantFilterPerc.

dirs:

Object of class character. Based on a directory given at instantiation of the object, it contains a vector of several directories containing all relevant GS Mapper project files.

experimentData:

Object of class MIAME. Contains details of the experiment.

annotation:

Object of class character Label associated with the annotation package used in the experiment.

protocolData:

Object of class AnnotatedDataFrame. Contains additional information about the samples.

.__classVersion__:

Object of class Versions. Remembers the R and R453Toolbox version numbers used to created the MapperSet instance.

Extends

Class eSet, directly. Class VersionedBiobase, by class "eSet", distance 2. Class Versioned, by class "eSet", distance 3.

Methods

setVariantFilter(object):

Sets the filter to display only those variants, whose coverage (in percent) in forward and reverse direction in at least one sample is higher than the given value.

getVariantPercentages(object)

Computes the coverage for every variant over all reads (forward and/or reverse) and for each sample.

annotateVariants(object):

Annotates given genomic variants. See annotateVariants for details.

htmlReport(object):

Exports all (filtered) variant data into a html report. See htmlReport for details

getReadStatus(object):

Reads the file "454ReadStatus.txt" in the GSM project directory which contains information about the alignment of each read (chr, pos, strand, etc.)and returns its content in a dataframe.

Author(s)

Christoph Bartenhagen

See Also

AVASet, annotateVariants, htmlReport, setVariantFilter, getVariantPercentages

Examples

# sum up class structure
showClass("MapperSet")

# load a GS Mapper dataset containing 3 samples and 111 variants
data(mapperSetExample)
mapperSetExample

# show contents of assay, feature and pheno data
assayData(mapperSetExample)
fData(mapperSetExample)
pData(mapperSetExample)

R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.