normR v1.19.3

First ever GitHub release using builds from bioc devel 3.14

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CHANGES IN VERSION 1.19.3

• Changed deprecated 'GenomeInfoDb::fetchExtendedChromInfoFromUCSC' to
  'GenomeInfoDb::getChromInfoFromUCSC' in R/methods.R

CHANGES IN VERSION 1.19.1

• Fixing R 4.1.0 _R_CHECK_LENGTH_1_LOGIC2 error in tests/testthat/utils.R:applyMap
  by using inherits() instead of class() to account for hadleyverse

CHANGES IN VERSION 1.13.4

• Recreation of Rd documentation files to fix R CMD check WARNING on Windows

CHANGES IN VERSION 1.13.3

• Fixing bamsignals-methods cross-reference that produced a warning in R CMD
  check on Windows

CHANGES IN VERSION 1.13.2

• Fixing errors in vignette using undefined symbol 'idx'

CHANGES IN VERSION 1.11.2

• Changed deprecated 'GenomeInfoDb::fetchExtendedChromInfoFromUCSC' to
  'GenomeInfoDb::getChromInfoFromUCSC' in tests

CHANGES IN VERSION 1.11.2

• Added correct CITATION

CHANGES IN VERSION 1.11.1

• Maintainer E-mail adress updated

CHANGES IN VERSION 1.3.1

FEATURES

• summary() output more concise
• getEnrichment() takes F for specifying a desired foreground
  component for standardization of the enrichment
• iterations argument allows running multiple fits with different
  starting values
• T Filter threshold can now be specified with minP argument for less
  stringent filtering
• Added a normR overview scheme to the vignette
• Qvalue computation improvement by specifying range for prop. of H_0

BUGFIXES
- Fixed the erroneous tiling of supplied GR objects in char,char,GRanges
- diffR() is more robust by doing a label-switched fit also

CHANGES IN VERSION 1.0.0

• Initial Bioconductor 3.3 Release

CHANGES IN VERSION 0.99.7

BUGFIXES

• Binning "genome" now reports correct genomic coordinates
  enrichR,character,character,data.frame-method
  diffR,character,character,data.frame-method
  regimeR,character,character,data.frame-method
• Correcting counting on supplied ranges object with a warning displayed
  if they are not equally sized
• getEnrichment() allows for adjusting the foreground now
• T Filter threshold is now controlled with the minP argument in main
  methods

CHANGES IN VERSION 0.99.6

FEATURES

• summary() for NormRFit instances shows now percentage of bins at each
  significance level
• getEnrichment() takes argument for computing a non-standardized
  enrichment

PERFORMANCE

• SIMD optimization for OpenMP >= ver4

CHANGES IN VERSION 0.99.5

FEATURES

• summary() for NormRFit instances of types "diffR" and "regimeR" now
  shows componentwise test results

BUGFIXES

• Removing MAKEFLAG "-D_GLIBCXX_PARALLEL" because it is experimental

CHANGES IN VERSION 0.99.4

BUGFIXES

• Removing PKG_CPPFLAGS and PKG_LIBS variables from src/Makevars

CHANGES IN VERSION 0.99.3

BUGFIXES

• Fixing imports in roxygen2

CHANGES IN VERSION 0.99.2

FEATURES

• Vignette finished
• Documentation for NormRFit-class & NormRCountConfig-class updated

BUGFIXES

• deploy.log removed

CHANGES IN VERSION 0.99.1

FEATURES

• Added examples for normr-methods, BamCountConfig-class & NormRFit-class
• Moved all documentation to one manpage (normr.Rd)
• Vignette: knitr-based vignette for normr finished
• exportR(): Export NormRFit objects to bed, bedGraph and bigWig
• plot(): Produce a small diagnostic plot for NormRFit objects
• diffR(): Intersection of results for switched labels increases
  specificity

BUGFIXES

• Removed deploy.log
• Fixed build errors and warnings
• Fixed failing test

CHANGES IN VERSION 0.99.0

FEATURES

• huge performance speedup by data compression to unique tupels only
• Kahan summation for log posterior summation to reduce numerical error
• Standardized enrichment computation in C++. This enrichment can be well
  compared between various ChIP-seq experiments
• exportR() function provides methods to export results of fits as a
  region bed file or bigWig track of standardized enrichment

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For more information on version numbering conventions see