Kataegis is a localized hypermutation occurring when a region is enriched in somatic SNVs. Kataegis can result from multiple cytosine deaminations catalyzed by the AID/APOBEC family of proteins. This package contains functions to detect kataegis from SNVs in BED format. This package reports two scores per kataegic event, a hypermutation score and an APOBEC mediated kataegic score. Yousif, F. et al.; The Origins and Consequences of Localized and Global Somatic Hypermutation; Biorxiv 2018 .
News
SeqKat 0.0.6
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Removed 'SeqKat' in single quotes from the Title field of the DESCRIPTION file as requested by CRAN maintainer
Removed 'SeqKat' in single quotes from the start of the Description field of DESCRIPTION file as requested by CRAN maintainer
Added DOI to Description field of DESCRIPTION file as requested by CRAN maintainer
Added 'SeqKat' in single quotes Title and Description field of DESCRIPTION file as requested by CRAN maintainer
Modified the seqkat() function to not setwd() into the output.dir set by the user since you aren't allowed to chdir to /tmp on CRAN test servers
Switched "." in tests to tempdir() to avoid writing in the homedir of CRAN test servers
Wrote runnable tests to replace the \dontrun{} tests and added RData files based on the bed file in the test directory for the intermediate functions to be tested with
SeqKat 0.0.5
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Added knitr to the Suggests and VignetteBuilder fields of the DESCRIPTION, causing changes to the vignette index which CRAN requires
Fixes for the Makevars file to support Solaris, as well as minor changes to the lookup symbols for the C++ functions due to changes in R 3.4.3
Added proper array size to char array to fix memory leak
Switching from rmarkdown to knitr for rendering the vignette
SeqKat 0.0.4
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Figured out which c++ flags are required to strip out unnecessary headers from the object files
Adding the correct vignette builder to the description, fixing docs and removing a bed file from the old location
Vignette fixes
Updating the docs with the new example from roxygen
Added an example dataset
SeqKat 0.0.3
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Allocating and deallocating the trinuc array properly
Adjusting how we instantiate Rcpp::NumericVector's since windows is bad at overloading Rcpp functions apparently
Moving doMC to the suggests section
Changed maintainer and added doParallel
Updated description and authors
Added Roxygen2 docs
Added chromosome length file for GRCh38
Added generate.trinucleotide.counts, a script to make the tn counts file
SeqKat 0.0.2
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Improved the docs/vignette
Added the get.trinucleotide.counts function to allow the user to generate their own count file (which supports hg38 now)
Added lots of error handling and refactored to allow for individual chrs and/or bed files to be handled (so HPCI can handle the parallelization better)
SeqKat 0.0.1
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Modified to allow the user to provide a file containing the lengths of the chromosomes for their desired reference, with a default file for hg19 stored in extdata
Fixing a bug where chromosomes with few SNVs try to write a list of lists to an output table
Added error handling and examples
Added documentation for the new main seqkat function, and added params for the ref.dir and bed.dir
Full restructure of SeqKat into a standard Rcpp package, with two extdata files (tn_count.txt and length_hg19_chr.txt)