NEWS

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normr 1.18.2

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

normr 1.18.1

• 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

normr 1.13.4

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

normr 1.13.3

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

normr 1.13.2

• Fixing errors in vignette using undefined symbol 'idx'

normr 1.13.1

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

normr 1.11.2

• Changed deprecated 'GenomeInfoDb::fetchExtendedChromInfoFromUCSC' to 'GenomeInfoDb::getChromInfoFromUCSC'
• Added correct CITATION

normr 1.11.1

• Maintainer E-mail adress updated

normr 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

normr 1.0.0

• Initial Bioconductor 3.3 Release

normr 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

normr 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

normr 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

normr 0.99.4

BUGFIXES

• Removing PKG_CPPFLAGS and PKG_LIBS variables from src/Makevars

normr 0.99.3

BUGFIXES

• Fixing imports in roxygen2

normr 0.99.2

FEATURES

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

BUGFIXES

• deploy.log removed

normr 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

normr 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