MMAPPR2data: MMAPPR2data: Example Data for MMAPPR2

In kjohnsen/MMAPPR2data: Sample Data for MMAPPR2

Description

Contains BAM files and indices for example use in MMAPPR2. The data is artificial, meant to simulate sequencing of the zebrafish slc24a5 gene in mutant and wild-type pools resulting from the cross of a novel mutant from a forward genetics screen with a wild-type line, as described in Hill et al. 2013.

Usage

exampleMutBam()

exampleWTbam()

goldenFasta()

goldenGFF()

Details

Besides BAM files and indices, the package also contains fasta and gtf files for just the region of the slc24a5 gene, which are also used in demonstrating MMAPPR2's functionality. They are based on the GRCz11 assembly and were obtained from Ensembl version 95.

Value

A BamFile object referencing a BAM file and its index.

A BamFile object referencing a BAM file and its index.

A path to the bgzipped slc24a5 fasta file

The path to the bgzipped GFF file

Functions

• exampleMutBam: Easy access to example mutant pool BAM file.

• exampleWTbam: Easy access to example wild-type pool BAM file.

• goldenFasta: Easy access to example fasta file for slc24a5 gene.

• goldenGFF: Easy access to example GFF file for slc24a5 gene.

Examples

mutFile <- exampleMutBam()
wtFile <- exampleWTbam()
goldenFasta <- goldenFasta()
goldenGFF()

kjohnsen/MMAPPR2data documentation built on Sept. 6, 2019, 12:58 p.m.