BBCAnalyzer (version 1.2.0)

BBCAnalyzer-package: \Sexpr[results=rd,stage=build]{tools:::Rd_package_title("#1")}BBCAnalyzerBBCAnalyzer: an R/Bioconductor package for visualizing base counts

Description

\Sexpr[results=rd,stage=build]{tools:::Rd_package_description("#1")}BBCAnalyzerBBCAnalyzer 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

\Sexpr[results=rd,stage=build]{tools:::Rd_package_DESCRIPTION("#1")}BBCAnalyzerThis package was not yet installed at build time. 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.

\Sexpr[results=rd,stage=build]{tools:::Rd_package_indices("#1")}BBCAnalyzer Index: This package was not yet installed at build time.

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.

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)