Changes in Version 1.47.2 o Added a check to see if genomdat is a one-dimensional array Changes in Version 1.47.1 o Added importFrom("grDevices", "dev.cur", "dev.interactive", "dev.new") and importFrom("utils", "data") to NAMESPACE to resolve warnings 1.41.3 became 1.42.0, 1.44.0 and 1.46.0 in Bioconductor 3.1, 3.2 & 3.3 ---------------------------------------------------------------------- Changes in Version 1.41.3 o Address the "malformed Description field" NOTE. Changes in Version 1.41.2 o change in segment to remove "no visible binding for global variable" NOTE during R CMD check Changes in Version 1.41.1 o add as.numeric to cumsum call in plotSample to address integer overflow 1.37.4 became 1.38.0 in Bioconductor 2.14 & 1.40.0 in Bioconductor 3.0 ---------------------------------------------------------------------- Changes in Version 1.37.4 o segment function now returns the weights used if weights are given. Changes in Version 1.37.3 o Changed default main, xlab, ylab options in plotSample to NULL to allow for empty strings to produce blank labels. Changes in Version 1.37.2 o Version 1.37.1 appears to be a system change to add vignettes directory o Changed cex option in plotSample and main, xlab, ylab options in zoomIntoRegions to be customizable. 1.35.1 became 1.36.0 in Bioconductor 2.13 & =1.36.0 now ------------------------------------------------------ Changes in Version 1.35.1 o update cytoBand data to match the goldenPath hg19 file 1.33.1 became 1.34.0 in Bioconductor 2.12 & =1.35.0 now ------------------------------------------------------ Changes in Version 1.33.1 o changes to smooth.CNA. Looping over chromosomes done within fortran and calculate median of nbhd only when needed. Change R code to match. 1.31.1 became 1.32.0 in Bioconductor 2.11 & =1.33.0 now ------------------------------------------------------ Changes in Version 1.31.1 o use function segments in plots instead of lines in a loop 1.29.2 became 1.30.0 in Bioconductor 2.10 & =1.31.0 now ------------------------------------------------------ Changes in Version 1.29.2 o Dropped startup message about data format. Changes in Version 1.29.1 o added additional details the smooth.CNA help function o made sure that CNA orders data correctly when chrom is an ordered variable with both integer and character values (i.e. X or Y). 1.27.2 became 1.28.0 in Bioconductor 2.9 & =1.29.0 now ------------------------------------------------------ Changes in Version 1.27.2 o segment function gets default.DNAcopy.bdry internaly instead of assuming DNAcopy is loaded. Allows for loading package by NAMESPACE only. o xmaploc now works for samplebychrom and chrombysample also. Changes in Version 1.27.1 o Don't further segment if all values in the current segment are the same. o Use is.finite in functions instead of is.na(.) & !(abs(.)==Inf) 1.25.1 became 1.26.0 in Bioconductor 2.8 & =1.27.0 now ------------------------------------------------------ Changes in Version 1.25.1 o House keeping: changed the URL for cytoband and removed Columbia email 1.23.8 became 1.24.0 in Bioconductor 2.7 & =1.25.0 now ------------------------------------------------------ Changes in Version 1.23.8 o Added getbdry to exported functions in NAMESPACE Changes in Version 1.23.7 o Versions 1.23.4 to 1.23.6 were changes made to use file based data. This needed changing CNA and DNAcopy objects to S4 classes which was too much of a paradigm shift for users. So changes are undone here. o Change default smooth.region to 10 in smooth.CNA o Added function plotSample for whole genome plot of a single sample. o Fixed the is.integer to is.numeric in subset functions. o CNA accomodates data.frames (as.matrix not needed) and presorted data. Changes in Version 1.23.3 (same fix applied in v1.22.1) o Fixed weird bug in smoothCNA.f triggered when there are at most 2*smooth.region (default smooth.region=2) markers in a chromosome. Changes in Version 1.23.2 o row numbers of the segments are automatically returned as the object segRows in the output. The print method shows it if showSegRows=TRUE. Changes in Version 1.23.1 o Added zoomIntoRegion function. o Added an option to return the row numbers of the segments. 1.21.6 became 1.22.0 in Bioconductor 2.6 & =1.23.0 now ------------------------------------------------------ Changes in Version 1.21.6 o Fixed indexing bug (i <= k or i > n-k, not and) in smoothCNA.f Changes in Version 1.21.5 o ADDED packageStartupMessage THAT CNA DATA FORMAT WILL CHANGE o changed filename of NEWS to CHANGES; file format didn't work with news o changed function .First.lib to .onLoad o in the function CNA, changed code for ordering by chrom and maploc because of "na.last=NA" slowed it down terribly o removed the unnecessary rownames command in CNA Changes in Version 1.21.4 o moved CHANGES file to inst/NEWS o documentation of CNA and segment say that missing values will be removed Changes in Version 1.21.3 o forgot to deallocate memory in the new code Changes in Version 1.21.2 o changed the code for htmaxp & hwtmaxp for the hybrid Changes in Version 1.21.1 o changed our affiliations in the vignette 1.19.6 became 1.20.0 in Bioconductor 2.5 & =1.21.0 now ------------------------------------------------------ Changes in Version 1.19.6 o added function glFrequency to calculate gains and losses Changes in Version 1.19.5 o Changed smooth.CNA from all R to Fortran backbone Changes in Version 1.19.4 o Fixed infinite loop when the logratio is constant across a segment Changes in Version 1.19.3 o Redundancy check by Henrik Bengtsson o Bioconductor fixes (license version, BiocViews etc.) Changes in Version 1.19.2 o Fixed a rarely triggered bug in the new code Changes in Version 1.19.1 o Faster algorithm to compute the CBS maximum t-statistic 1.17.5 became 1.18.0 in Bioconductor 2.4 & =1.19.0 now ------------------------------------------------------ Changes in Version 1.17.5 o For weighted CBS return weighted segment means (not ordinary mean). Changes in Version 1.17.4 o Bug fixes to wtermp code and how it's called in wfindcpt. Changes in Version 1.17.3 o Weighted segmentation code added. Weights per probe can be used. Changes in Version 1.17.1 o NAMESPACE file added and man pages fixed to reflect it. 1.15.4 became 1.16.0 in Bioconductor 2.3 & =1.17.0 now ------------------------------------------------------ Changes in Version 1.15.4 o make sure there are at least 10 obsns when t-stat threshold is used Changes in Version 1.15.3 o the minimum width of segment is user selectable (argument min.width). Changed from the fixed value of 2 based on user demand. Max value 5. Changes in Version 1.15.2 o changed to a faster algorithm for calculating the max t-statistic o changed to a faster code for undoing edge effects (redundant perm) o added basic functions exon.segment and exon.changepoint (workhorse) These functions are used for finding a translocation using binary segmentation. The data for this should be properly normalized. o fortran code re-arranged into different files Changes in Version 1.15.1 o updated the call to get(getOption("device")) to use dev.new 1.13.3 became 1.14.0 in Bioconductor 2.2 & =1.15.0 now ------------------------------------------------------ Changes in Version 1.13.3 o Added segments.summary to give the median, sd & mad for each segment. Changes in Version 1.13.2 o Modified the p-value function to replace p > 1 with 1. Changes in Version 1.13.1 o Modified the p-value function. Added pseudo confidence intervals for the change-points. o Windowing option has been removed (R & fortran code modified). 1.11.2 became 1.12.0 in Bioconductor 2.1 & =1.13.0 now ------------------------------------------------------ Changes in Version 1.11.2 o Added a p-value function for the change-points. This is based on binary segmentation and not necessarily correct but gives an idea of the relative importance of the change-points. Changes in Version 1.11.1 o Changed Venkat's affiliation from MSKCC to Columbia University 1.9.3 became 1.10.0 in Bioconductor 2.0 & =1.11.0 now ----------------------------------------------------- Changes in Version 1.9.3 o Added warning that windowing will be deprecated in the next version. Changes in Version 1.9.2 o Added code to not bother with p-values and split the segment when the maximal T is large (p-value will be tiny if T > 7). o Added code to not split when the maximal T is small (fixes a numerical problem where a constant large segment can have a significant split). Changes in Version 1.9.1 o The mod function in fortran inflicts serious time penalty -- code rewritten to fix it 1.5.3 became 1.6(8).0 in Bioconductor 1.8(9) & =1.9.0 now --------------------------------------------------------- Changes in Version 1.5.3 o Fixed the subset functions to enable sample re-ordering Changes in Version 1.5.2 o Bug fix in plot.DNAcopy (triggered only when #chrom=1) o Added information about stopping rule in the Vignette o Cytoband data from the goldenPath repository added for future plots Changes in Version 1.5.1 o Add a sequential stopping rule to declare change early o Bug fix - make the object from subset.DNAcopy of class DNAcopy ############################################################### ### ### ## E. S. Venkatraman is the new package maintainer ## ### ### ############################################################### 1.2.5 became 1.4.0 in Bioconductor 1.7 & =1.5.0 in the development branch ------------------------------------------------------------------------- Changes in Version 1.2.5 o Updated the vignette to include references to additional features. Changes in Version 1.2.4 o Seg fault occurs if window.size is set when hybrid method is used. Fixed by setting window.size to be NULL in the function segment. o Added options to plot command to draw line at y=0 and control its color and lwd of all lines. o If ylim is missing it's calculated from all the data instead of just the first sample. Changes in Version 1.2.3 o Modifications to the plot function to make par("ask") behave better. Changes in Version 1.2.2 o Modified the plot function. X-axis is either the index or (cumulative) map location. Incorporate col, pch, ylim etc. to provide better control over plots. Changes in Version 1.2.1 o Added the hybrid method for computing p-values to determine splits. This speeds up the computations considerably and so has been made the default.