MapperSet-class {R453Plus1Toolbox} | R Documentation

## Class to Contain GS Reference Mapper Output

### 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)

[Package R453Plus1Toolbox version 1.40.0 Index]