Version: 1.23.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Add use.names and header options in exportC Version: 1.23.0 Category: BUG FIXES Text: Fix bug in getExpectedCountsMean for non-symmetrical data Version: 1.23.0 Category: BUG FIXES Text: Deal with NA in getPearson function Version: 1.23.0 Category: BUG FIXES Text: Fix bug in normLGF leading to non symmetrical matrices Version: 1.17.1 Category: NEW FEATURES Text: New getPearsonMap function. Will generate the correlation map used by the pca analysis Version: 1.17.1 Category: NEW FEATURES Text: The pca.hic function is now able to detect and to assign the A/B compartment if a gene annotation is provided Version: 1.17.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: update of reduce method for HTClist object Version: 1.17.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: update of the getExpectedCounts function with two methods ; loess and mean. The mean method allows to estimated the expected counts using the mean of diagonal matrices. The method is adviced in case of high resolution maps when the loess smoothing can take time and might not give good results Version: 1.17.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: By default, obs/exp maps are now centered before calculated the pearson correlation map. This allow correlation of small values to be as valuable as correlation of big values Version: 1.17.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: asRangedData from importC is now deprecated due to rtracklayer change Version: 1.17.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: normPerExpected function now reports 0 instead of NA to avoid error in correlation calculation Version: 1.17.1 Category: BUG FIXES Text: Fix bug in directionalityIndex. The input count matrix is converted into a dense matrix before calculation Version: 1.15.1 Category: NEW FEATURES Text: new saveContactMaps function Version: 1.15.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Change default behavior of binningC function to use sum of intervals instead of median Version: 1.15.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Hi-C color are now defined as a vector, so that more than 3 colors can be used to for the gradient Version: 1.15.1 Category: BUG FIXES Text: Fix bug in import.my5C in reading file Version: 1.13.2 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Change in the way the interaction matrix is loaded. During the import, the lazyload option will force the data to be stored as triangular matrix. Note that a symmetric matrix is not triangular by construction. Then, to avoid any error in the data processing, the triangular matrix is always converted into symmetrical matrix before being returned by the intdata method. Version: 1.13.2 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of track display in mapC function. Off-set plot of adjacent features Version: 1.13.2 Category: BUG FIXES Text: Bug fixed in quality control function when empty maps are used Version: 1.13.2 Category: BUG FIXES Text: Bug fixed when plotting empty matrix Version: 1.13.1 Category: NEW FEATURES Text: Export methods getCombinedContacts, getCombinedIntervals for HTClist objects Version: 1.13.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: getCombinedContact is now able to merge HTCexp objects for non complete HiTClist objects. Missing maps are replaced by NA matrices Version: 1.13.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of isComplete, isPairwise, getCombinedIntervals methods for Hi-C data with no intrachromosomal maps Version: 1.13.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: When the maxrange argument is set in the mapC function, all maps are displayed on the same scale so that they can be compared to each other Version: 1.13.1 Category: BUG FIXES Text: Bug fixed in mapC with the contact map is empty Version: 1.13.1 Category: BUG FIXES Text: Bug fixed in seqlevels(HTClist) method Version: 1.11.4 Category: NEW FEATURES Text: New directionalyIndex function as a first step of TADs detection Version: 1.11.4 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: new forcePairwise method for HTClist or HTCexp objects. The methods reverse the forceSymmetrical method. Useful for plotting function. Version: 1.11.4 Category: BUG FIXES Text: Bug in mapC for Pairwise Hi-C map Version: 1.11.3 Category: BUG FIXES Text: Bug in setEnvDisplay report by S. Thomas. Change decimal to 5 to avoid layout of size 0 for small chromosomes Version: 1.11.1 Category: NEW FEATURES Text: Changes in forceSymmetric method on HTCexp object. The default is now to sum up both upper and lower maps. Version: 1.11.1 Category: BUG FIXES Text: Bug in import.my5C function Version: 1.9.6 Category: BUG FIXES Text: Bug in import.my5C function Version: 1.9.5 Category: NEW FEATURES Text: The normLGF function can now be applied both on intra and inter-chromosomal maps Version: 1.9.5 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Access the contact map is now ALWAYS performed using chromosomes' name such as ygi/xgi, i.e. rownames/colnames of contact maps Version: 1.9.5 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of the setGenomicFeatures method and speed improvment Version: 1.9.5 Category: BUG FIXES Text: Update of isComplete method Version: 1.9.5 Category: BUG FIXES Text: Update of import functions Version: 1.9.4 Category: NEW FEATURES Text: ICE normalization can now be applied on both HTCexp and HTClist objects Version: 1.9.4 Category: NEW FEATURES Text: New methods for HTClist-class : isComplete, isPairwise, forcePairwise, forceSymmetric Version: 1.9.4 Category: NEW FEATURES Text: New methods for HTCexp-class : forceSymmetric Version: 1.9.4 Category: NEW FEATURES Text: New methods (not exported) for HTClist-class : getCombinedIntervals, getCombinedContacts Version: 1.9.4 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of the binningC method. Improvement of speed and memory usage. The binningC function can now be applied on Hi-C data (or any already binned data). The goal is to move from a very high resolution map (for instance 40kb) to a lower resolution ( for instance 1Mb) by aggregationg and summing the bins. Version: 1.9.4 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of the importC/exportC functions which are now based on a new format (list with interactor1/interactor2/count + BED files). This format is recommanded to store sparse data because only the non null values are exported/imported. Version: 1.9.4 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of the import.my5C/export.m5C functions. Only the matrix format is now supported. For the list format, see the importC/exportC functions. Version: 1.9.4 Category: BUG FIXES Text: Bug fixed in divide method Version: 1.9.3 Category: NEW FEATURES Text: getRestrictionFragmentsPerChromosome Version: 1.9.3 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update output of summary method to add the seqlevels of both interactors Version: 1.9.3 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Speed improvement; seqlevels Version: 1.9.3 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update import.my5C function Version: 1.9.3 Category: BUG FIXES Text: Fix bug in HTCexp constructor. Only intrachromosomal data can be force to be symmetrical Version: 1.9.3 Category: BUG FIXES Text: Fix bug in summary function for HTClist object Version: 1.9.3 Category: BUG FIXES Text: Fix bug in mapC function, in case of empty matrices (only zero values) Version: 1.7.11 Category: NEW FEATURES Text: Update NAMESPACE for BioC 2.14 Version: 1.7.11 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Version: 1.7.11 Category: BUG FIXES Text: Fix a bug in the getRestrictionSitesPerChromosome and matchPattern function (fixed=TRUE). If FALSE, all 'N' are reported. Version: 1.7.5 Category: NEW FEATURES Text: Update for BioC 2.14 Version: 1.7.5 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Add fit.out parameter in the plotIntraDist to remove the outliers during the regression Version: 1.7.5 Category: BUG FIXES Text: Version: 1.7.4 Category: NEW FEATURES Text: Version: 1.7.4 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: New parameter for normICE - spars.filter, to filter out the more sparse bins before normlization Version: 1.7.4 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Change the parameters of getAnnotatedRestrictionSites and setGenomicFeatures functions Version: 1.7.4 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of the setGenomicAnnotation function to fit with the original HiCNorm method Version: 1.7.4 Category: BUG FIXES Text: isSymmetrix - NA values Version: 1.7.4 Category: BUG FIXES Text: Bug in definition of upstream and downstream flanking region for a restriction site in getAnnotatedRestrictionSites Version: 1.7.3 Category: NEW FEATURES Text: Add new normalization method for Hi-C data from Hu et al (HiCNorm). This method is based on linear regression model between interaction counts and sources of bias such as GC content, mappability, fragment length, etc. See normLGF(), setGenomicFeatures(), getAnnotatedRestrictionSites(). Version: 1.7.3 Category: NEW FEATURES Text: Add new normalization method for Hi-C data from Imakaev et al.(ICE). The ICE procedure is an iterative normalization method used to remove any bias from HiC data. Version: 1.7.3 Category: NEW FEATURES Text: Add 'summary' method for HTCexp and HTClist objects Version: 1.7.3 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Improve quality control methods based using sparse data Version: 1.7.3 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Change method option for normPerTrans methods. The 'mean' method is in fact a 'max' method Version: 1.7.3 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of the export.my5C list format Version: 1.7.3 Category: BUG FIXES Text: max (na.rm=TRUE) in mapC function Version: 1.5.2 Category: NEW FEATURES Text: Efficient memory matrix representation using the Matrix package. The memory usage for big sparse matrix is improved by a factor 7. However, some operation are much slower based on the Matrix implementation. Thus, for some task as the plotting function, the Matrix are converted in standard matrix based object Version: 1.5.2 Category: NEW FEATURES Text: 'show' and 'detail' method for HTClist object Version: 1.5.2 Category: NEW FEATURES Text: 'c(x, ...)' method for HTCexp and HTClist objects Version: 1.5.2 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The option mask.data from the mapC function is deprecated Version: 1.5.2 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of parallel computation for some functions (import, normalize) Version: 1.5.2 Category: BUG FIXES Text: Bug Fixe in import.my5C for ChrM Version: 1.5.1 Category: BUG FIXES Text: Fix bug in HTCexp contructor for matrix of dim 1 Version: 1.5.1 Category: BUG FIXES Text: Fix bug in import.my5C for matrix of dim 1 Version: 1.5.1 Category: BUG FIXES Text: Fix bug for title display on HTCexp plots Version: 1.5.1 Category: BUG FIXES Text: Fix bug in HiTClist plot due to chromosome order Version: 1.5.1 Category: BUG FIXES Text: Correct errors in the man pages Version: 1.3.3 Category: NEW FEATURES Text: Add PCA function on Hi-C interaction map as in Lieberman-Aiden et al. 2009 Version: 1.3.3 Category: BUG FIXES Text: Error in constructor when the interaction map has a dim = 1 Version: 1.3.2 Category: NEW FEATURES Text: New visualization for HTClist objects Version: 1.3.2 Category: NEW FEATURES Text: New methods for HTClist objects Version: 1.3.2 Category: NEW FEATURES Text: New HTClist class to manage list of HTCexp object (basically Hi-C data) Version: 1.3.2 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of all man pages Version: 1.3.2 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of the Nora_5C data. E14 and MEF are now HTClist objects Version: 1.3.2 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of the importC/exportC function. The standard format is now matrix-based. This seems to be the most commonly used format. Version: 1.3.2 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of all mapC methods. The view parameter is removed. The HTCexp object are now displayed in the triangle view, whereas the HTClist are displayed in the heatmap view Version: 1.3.1 Category: NEW FEATURES Text: MAJOR RELEASE : replace all GenomeIntervals objects by GRanges ones in order to improve the compatibility with other HT BioC packages Version: 1.3.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The ExtractRegion method has a new MARGIN parameter. The idea is the same than for any apply function. If MARGIN is equal to 1 (resp. 2, resp. c(1,2)), the region is extracted from the 'x' (resp. 'y', resp. both) intervals Version: 1.3.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Plot function. When two HTCexp objects are plot together, only the intersection of the 'x' and 'y' intervals are used. Version: 1.3.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The 'range' method now returns a GRanges object Version: 1.3.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Changes in the data windowing for the extreme bins Version: 1.3.1 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: mapC requires a HTCexp object only. Objects from the matrix class are no longer allowed Version: 1.3.1 Category: DEPRECATED AND DEFUNCT Text: seq_name is now deprecated Version: 1.3.1 Category: DEPRECATED AND DEFUNCT Text: export and normPerZscore are now defunct Version: 1.3.1 Category: BUG FIXES Text: exportC. Bug fixed in bin coordinates Version: 1.3.1 Category: BUG FIXES Text: CQC. Bug fixed with NA values Version: 1.3.1 Category: BUG FIXES Text: mapC. Bug fixed in the visualization of annotation features. Select the annotation in the same chromosome space before plotting. Version: 1.3.1 Category: BUG FIXES Text: mapC. Bug fixed in the visualization of count values for interchromosomal data Version: 1.1.3 Category: NEW FEATURES Text: Adding CITATION file Version: 1.1.3 Category: DEPRECATED AND DEFUNCT Text: Update of getExpectedCount function to use the lowess() function (stats). The 'C' call in stats is now deprecated Version: 1.1.2 Category: NEW FEATURES Text: New package vignette Version: 1.1.2 Category: NEW FEATURES Text: Add new normalization method - normPerTrans Version: 1.1.2 Category: NEW FEATURES Text: Add importC and exportC function, to load and import csv file Version: 1.1.2 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The CQC function now returns a matrix Version: 1.1.2 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Simplify getExpectedCounts help page Version: 1.1.2 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Update of import.my5C function. Simplify the import for matrix data Version: 1.1.2 Category: DEPRECATED AND DEFUNCT Text: The export method is now replace by exportC. The standard csv format is now exported. Version: 1.1.2 Category: DEPRECATED AND DEFUNCT Text: The normPerZscore method is depracted. See normPerExpected instead Version: 1.1.2 Category: DEPRECATED AND DEFUNCT Text: Remove Bau et al. 5C dataset Version: 1.1.2 Category: BUG FIXES Text: isBinned. Fix bug for interchromosomal interactions Version: 1.1.2 Category: BUG FIXES Text: extracRegion. Add a chromosome parameter, and changes for interchromosomal data Version: 1.1.2 Category: BUG FIXES Text: binningC. Changes for interchromosomal maps Version: 1.1.2 Category: BUG FIXES Text: Sort xgi and ygi objects when the HTCexp constructor is called Version: 1.1.2 Category: BUG FIXES Text: Force the xgi and ygi objects to have some ids Version: 1.1.1 Category: NEW FEATURES Text: Include the Nora et al (Nature 2012) 5C dataset (GSE35721).Two mouse samples are included in the package ; male undifferentiated ES cells (E14, GSM873935) and male embryonic fibroblasts (MEF, GSM873924). Only the cis interaction maps chrX vs chX are provided.