BBCAnalyzer-package {BBCAnalyzer} | R Documentation

## BBCAnalyzer: an R/Bioconductor package for visualizing base counts

### Description

BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.

### Details

Package: | BBCAnalyzer
Type: | Package
Title: | BBCAnalyzer: an R/Bioconductor package for visualizing base counts
Version: | 1.12.0
Date: | 2016-01-26
Author: | Sarah Sandmann
Maintainer: | Sarah Sandmann <sarah.sandmann@uni-muenster.de>
Description: | BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.
License: | LGPL-3
Imports: | SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings
Suggests: | BSgenome.Hsapiens.UCSC.hg19
biocViews: | Sequencing, Alignment, Coverage, GeneticVariability, SNP
NeedsCompilation: | no
git_url: | https://git.bioconductor.org/packages/BBCAnalyzer
git_branch: | RELEASE_3_8
git_last_commit: | 97364cf
git_last_commit_date: | 2018-10-30
Date/Publication: | 2018-10-30

In the use case of medical diagnostics, a tool performing detailed analyses of those locations where mutations may be expected – but not always called – appears to be most useful. Low allele frequency and bad base quality do often explain a lacking call. Yet, this information is not included in a VCF-file and difficult to obtain from other existing tool. Furthermore, with regards to the comparison of different sequencing techniques, it seems helpful to have a tool for visualizing the background at a selection of locations where e.g. one technique calls a variant but another technique does not.

BBCAnalyzer (Bases By CIGAR Analyzer) is a tool for visualizing the number of counted bases, deletions and insertions at any given position in any genome in comparison to the reference bases. Relative frequencies, base qualities, known mutations or polymorphisms and called variants may be included into the plots as well.

Index of help topics:

    BBCAnalyzer             BBCAnalyzer: an R/Bioconductor package for
                            visualizing base counts
    analyzeBases            Analyze the bases at all previously defined
                            positions
    analyzeBasesPlotOnly    Plots the number of reads at all previously
                            defined positions

The package contains two functions - `analyzeBases` and `analyzeBasesPlotOnly`. The major use of BBCAnalyzer is documented in the description of the function `analyzeBases`. The function `analyzeBasesPlotOnly` serves as an extension.

### Author(s)

Sarah Sandmann

Maintainer: Sarah Sandmann <sarah.sandmann@uni-muenster.de>

### References

More information on the bam format can be found at: http://samtools.github.io/hts-specs/SAMv1.pdf

### See Also

`analyzeBases`, `analyzeBasesPlotOnly`

### Examples

    library("BSgenome.Hsapiens.UCSC.hg19")
    ref_genome<-BSgenome.Hsapiens.UCSC.hg19

    output<-analyzeBases(sample_names=system.file("extdata","SampleNames_small.txt",package="BBCAnalyzer"),
                         bam_input=system.file("extdata",package="BBCAnalyzer"),
                         target_regions=system.file("extdata","targetRegions_small.txt",package="BBCAnalyzer"),
                         vcf_input="",
                         output=system.file("extdata",package="BBCAnalyzer"),
                         output_pictures=system.file("extdata",package="BBCAnalyzer"),
                         known_file="",
                         genome=ref_genome,
                         MQ_threshold=60,
                         BQ_threshold=50,
                         frequency_threshold=0.01,
                         qual_lower_bound=58,
                         qual_upper_bound=63,
                         marks=c(0.01),
                         relative=TRUE,
                         per_sample=TRUE)

[Package BBCAnalyzer version 1.12.0 Index]