MapperSet: Creating a MapperSet

Description

This function imports a project of Roche's GS Reference Mapper Software. It stores all information into an instance of the Biobase ExpressionSet.

Usage

MapperSet(dirs, samplenames)

Arguments

dirs

A character vector containing all sample directories (i.e. directories that contain the files "mapping/454HCDiffs.txt" (required), "mapping/454ReadStatus.txt" (optional), "mapping/454NewblerMetrics.txt"(optional)).

samplenames

A character vector containing samplenames. The order and number of samplenames must be consistent with the filenames to ensure the correctness of the MapperSet. If no samplenames are given, the filenames are used for naming.

Value

An instance of the MapperSet.

Details

An instance of the MapperSet is derived from the Biobase eSet and thus structured into

1. assayData

variantForwCount/variantRevCount:: Contain the number of reads with the respective difference in forward/reverse direction.
totalForwCount/totalRevCount:: Contain the total coverage for every variant in forward/reverse direction.

2. featureData

chromosome, start/end:: Give the location of each variant.

referenceBases/variantBase:

Show the bases changed in each variant.

regName:

The name of the region (gene) where the variant is located.

knownSNP:

Lists Ensembl variant-ids for known SNPs (if any).

3. phenoData

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

Examples

Run this code

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