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NEWS
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NEWS
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CHANGES IN VERSION 1.18.2
-------------------------
o Changed deprecated 'GenomeInfoDb::fetchExtendedChromInfoFromUCSC' to
'GenomeInfoDb::getChromInfoFromUCSC' in R/methods.R
CHANGES IN VERSION 1.18.1
-------------------------
o 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
-------------------------
o Recreation of Rd documentation files to fix R CMD check WARNING on Windows
CHANGES IN VERSION 1.13.3
-------------------------
o Fixing bamsignals-methods cross-reference that produced a warning in R CMD
check on Windows
CHANGES IN VERSION 1.13.2
-------------------------
o Fixing errors in vignette using undefined symbol 'idx'
CHANGES IN VERSION 1.13.1
-------------------------
o Changed deprecated 'GenomeInfoDb::fetchExtendedChromInfoFromUCSC' to
'GenomeInfoDb::getChromInfoFromUCSC'
CHANGES IN VERSION 1.11.2
-------------------------
o Changed deprecated 'GenomeInfoDb::fetchExtendedChromInfoFromUCSC' to
'GenomeInfoDb::getChromInfoFromUCSC'
CHANGES IN VERSION 1.11.2
-------------------------
o Added correct CITATION
CHANGES IN VERSION 1.11.1
-------------------------
o Maintainer E-mail adress updated
CHANGES IN VERSION 1.3.1
-------------------------
FEATURES
o `summary()` output more concise
o `getEnrichment()` takes `F` for specifying a desired foreground
component for standardization of the enrichment
o `iterations` argument allows running multiple fits with different
starting values
o T Filter threshold can now be specified with `minP` argument for less
stringent filtering
o Added a normR overview scheme to the vignette
o Qvalue computation improvement by specifying range for prop. of H_0
BUGFIXES
o Fixed the erroneous tiling of supplied GR objects in char,char,GRanges
o `diffR()` is more robust by doing a label-switched fit also
CHANGES IN VERSION 1.0.0
-------------------------
o Initial Bioconductor 3.3 Release
CHANGES IN VERSION 0.99.7
-------------------------
BUGFIXES
o 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
o Correcting counting on supplied ranges object with a warning displayed
if they are not equally sized
o getEnrichment() allows for adjusting the foreground now
o T Filter threshold is now controlled with the minP argument in main
methods
CHANGES IN VERSION 0.99.6
-------------------------
FEATURES
o summary() for NormRFit instances shows now percentage of bins at each
significance level
o getEnrichment() takes argument for computing a non-standardized
enrichment
PERFORMANCE
o SIMD optimization for OpenMP >= ver4
CHANGES IN VERSION 0.99.5
-------------------------
FEATURES
o summary() for NormRFit instances of types "diffR" and "regimeR" now
shows componentwise test results
BUGFIXES
o Removing MAKEFLAG "-D_GLIBCXX_PARALLEL" because it is experimental
CHANGES IN VERSION 0.99.4
-------------------------
BUGFIXES
o Removing PKG_CPPFLAGS and PKG_LIBS variables from src/Makevars
CHANGES IN VERSION 0.99.3
-------------------------
BUGFIXES
o Fixing imports in roxygen2
CHANGES IN VERSION 0.99.2
-------------------------
FEATURES
o Vignette finished
o Documentation for NormRFit-class & NormRCountConfig-class updated
BUGFIXES
o deploy.log removed
CHANGES IN VERSION 0.99.1
-------------------------
FEATURES
o Added examples for normr-methods, BamCountConfig-class & NormRFit-class
o Moved all documentation to one manpage (normr.Rd)
o Vignette: knitr-based vignette for normr finished
o exportR(): Export NormRFit objects to bed, bedGraph and bigWig
o plot(): Produce a small diagnostic plot for NormRFit objects
o diffR(): Intersection of results for switched labels increases
specificity
BUGFIXES
o Removed deploy.log
o Fixed build errors and warnings
o Fixed failing test
CHANGES IN VERSION 0.99.0
-------------------------
FEATURES
o huge performance speedup by data compression to unique tupels only
o Kahan summation for log posterior summation to reduce numerical error
o Standardized enrichment computation in C++. This enrichment can be well
compared between various ChIP-seq experiments
o exportR() function provides methods to export results of fits as a
region bed file or bigWig track of standardized enrichment