Detection of Kataegis

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)

Reference manual

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install.packages("SeqKat")

0.0.6 by Paul C. Boutros, 10 months ago


Browse source code at https://github.com/cran/SeqKat


Authors: Fouad Yousif , Xihui Lin , Fan Fan , Christopher Lalansingh


Documentation:   PDF Manual  


GPL-2 license


Imports Rcpp

Depends on foreach, doParallel

Suggests testthat, doMC, rmarkdown, knitr

Linking to Rcpp


See at CRAN