1.0.0在用户级别上创建对象创建，以使Genoset，Bafset和CNSET函数都调用内部输入检查器和对象生成器函数initgenoset，而不是让GenoSet（）使用“类型” ARG创建所有3个对象。分段函数现在返回每个样品中包含一个RLE矢量的数据帧对象。这些效果具有相同的效果，即具有重复数据匹配未分段数据的尺寸，但要小得多。对于〜1K SNP6数组的数据集，使用此策略，LRR矩阵中的数据约为大小的0.8％。在所有方面，这些都可以视为AssayData中的另一个矩阵，但是在特殊情况下，利用其RunValue和Runlength形式中的数据很有用。为数据框定义的新方法允许用作用作测定元素：从genoset中获取基因组信息的Colmeans注释Dataframes，现在也可以在rangeddata上使用。Rangeddata和Genoset现在共享一些API，以使其更轻松。Rangeddata获得ChR和POS，Genoset获得名称，范围和元素长度。现在，Chrinfo，Chrindices，Genopos等都可以在任何一个对象类型上使用。POS和Genopos现在定义为开始和终点位置平均值的地板。 1.0.6 Substantial speed improvements for boundingIndices() and rangeSampleMeans. 1.1.7 Added loadGC function to get local GC content and version bump for bioC2.9 1.1.8 genomeOrder becomes toGenomeOrder which now takes and returns a GenoSet or RangedData rather than just returning the index to reorder such objects. locData<- now reorders the whole GenoSet and assures that all of the featureNames match. 1.1.9 Added support for big.matrix objects from bigmemory as assayDataElements 1.1.10 ***API Change*** list operator "[[" no longer used to subset by chromosome. It reverts back to extracting a column from pData like other eSets. chrIndices gains a "chr" argument that serves as a fast way to get the indices needed to subset rows by chromosome. 1.1.11 ***API Addition*** "k" argument to "[" can be used to subset from a specific assayDataElement. Numeric and character "k"s are allowed. assayDataElement(ds,k)[i,j] is the same as ds[i,j,k], but "i" can be a RangedData or RangesList. 1.1.12 assayDataElements can be integer matrices with levels that will serve as factors for now. Please see the help for convertToBigMatrix. 1.4.9 *** API Changes *** segTable on a DataFrame of Rle now has a "stack" argument to rbind the resulting list of data.frames of per-sample segments into on giant data.frame. A "Sample" column will be added to separate samples. The list of individual data.frames no longer has an "ID" column. Also, some refactoring to speed up this method. 1.4.10 segTable for Rle now optionally takes chrIndices table, start and stop from locData for speed. segTable for DataFrame uses this trick. Much faster. About 95% time reduction for a large dataset on a large chip. 1.4.19 *Minor API change* Rarely used (by me) method, orderedChrs, gone. It's just chrOrder(chrNames(x)) anyway. 'names' on GenoSet depricated. chrNames gives universal way to get chromosome names (i.e. names, seqlevels) for GenoSet, RangedData, GRanges. 1.7.7 genoPlot supports fast zooming into a chromosome with the 'xlim' arg. Subsets before plotting, which is much faster. Bugfix for odd issues with ... args and genoPlot on an Rle. 1.7.8 *Minor API change* genoPlot now takes numeric or Rle data as "y" rather than an index into the assayDataElement named in "element". Backwards compatible with a warning about the old usage being deprecated. RangedData or GRanges also now valid as "x". 1.9.8 GRanges everywhere! GenoSet now supports GRanges in the locData slot. All functions that take RangedData now also take GRanges. I have unified the API for GRanges, RangedData, and GenoSet to the point that GenoSet classes and the functions in the package are agnostic to the type of range object. I have not, however, fixed the contentious issue of using the "$" operator with GRanges to access elementMetadata. 1.9.10 Subsetting by location now only with GRanges and RangedData. Dropped RangesList to avoid weird errors about the RangedDataOrRangesListOrGRanges class union. Apparently the RangedDataOrGRanges class union is fine. I think RangesLists are not used often anyway. 1.9.11 GenoSet creation and featureNames<- no longer do make.names. 1.9.12 GenoSet creation and sampleNames<- no longer do make.names. 1.11.8 toGenomeOrder and isGenomeOrder for GRanges and RangedData now strict=TRUE by default, like for GenoSet 1.11.9 No more make.names on sampleNames in object initialization 1.11.22 CNSet and BAFSet are deprecated. See help("genoset-deprecated")