R News rCGH 1.1.8 -----------------------主要变化*集中度现在是在分段值的分布上估计的，所以在分割步骤之后。这意味着现在用户必须在EMnormalize()之前运行segmentCGH()。新特性* plotProfile()获得一个'showCopy'参数。当设置为“TRUE”时，配置文件的y轴将使用估计的拷贝数而不是log2ratio。* read()函数，用作rCGH-Object构造函数，有一个补充的'ploidy'参数。如果知道这个值，就可以用它来估计用拷贝数表示的增益和损失。默认值是2。*拷贝数估计也在所有表中报告，包括通过getCNset()访问的主by-probe表。rCGH 1.1.7 -----------------------新功能*用户现在可以指定哪些补充基因注释要通过byGeneTable()函数导出。允许的注释是由'AnnotationDbi'生物导体中的'select'方法支持的注释。 rCGH 1.1.6 ----------------------- BUG FIXES * Errors occured when mergin short segments, with respect to the minLen argument in segmentCGH(). rCGH 1.1.5 ----------------------- Cleaner version from 1.1.4. Should not give any warning due to functions masked by imported packages rCGH 1.1.4 ----------------------- NEW FEATURES * Read Illumina HumanOmniExpress: this function has been temporarily removed. Illumina data require to much memory for annotating probes when probe locations are missing in the data. rCGH 1.1.3 ----------------------- NEW FEATURES * Read Illumina HumanOmniExpress: see readIllumina() help in the rCGH documentation. * New rCGH-generic class for custom arrays: see readGeneric() help in the rCGH documentation. * Supports arrays designed according to hg18, hg19 (default) and hg38. To be specified by the user in the read functions and in the byGeneTable function. * plotProfile now as pCol and GLcol arguments, for points and gained/lost segments, respectively. rCGH 1.1.2 ----------------------- BUG FIXES * Major bug fixed in the view() function: one function was not properly called. rCGH 1.1.1 ----------------------- Not submitted! rCGH 1.1.0 ----------------------- New bioconductor devel versioning after release cycle. The first and corresponding bioconductor release version is 1.0.0. rCGH 0.99.10 ----------------------- BUG FIXES * In view() function: segment colors were not properly assigned. rCGH 0.99.9 ----------------------- BUG FIXES * In view() function: segment colors were not properly assigned. rCGH 0.99.8 ----------------------- BUG FIXES * Error when merging probes with duplicated locations on Agilent CytoGenomics 3.0: fixed. rCGH 0.99.7 ----------------------- SIGNIFICANT USER-VISIBLE CHANGES * byGeneTable() is not a S4 method anymore but S3: as argument, it takes a segmentation table exported from a rCGH object, and not the object itself. As a consequence, byGeneTable() can be used on any segmentation table of the same form as those exported from a rCGH object. * The full by-gene table is not stored in rCGH object, but built then exported on the fly, using byGeneTable(). * Supplementary argument in getSegTable(): minLen allows the user to specify the minimal segment length, in Kb. Segments shorter than this value are merged before the segmentation table is exported. The original table is still stored in the rCGH object. * New features in plotProfile() and multiplot(): one or multiple genes can be tagged. As for getSegTable(), the minimal segment length (in Kb) can be specified. * Server version for the interactive viewer is described in the vignette. BUG FIXES * byGeneTable: . In the exported by-gene table, the corresponding segment lengths were not properly reported. . Errors occured when a gene was covered by 2 segments. rCGH 0.99.6 ----------------------- SIGNIFICANT USER-VISIBLE CHANGES * New cytoScan example file * Updated vignette * The rCGH version used is stored in rCGH objects for traceability NON-VISIBLE CHANGES * Supplementary unittests rCGH 0.99.5 ----------------------- SIGNIFICANT USER-VISIBLE CHANGES * R-3.2.1 is the minimal required version rCGH 0.99.4: First release! ----------------------- SIGNIFICANT USER-VISIBLE CHANGES * No changes NEW FEATURES * New BUG FIXES * No changes classified as 'bug fixes' under active development)