版本变化1.27.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - o GenoSet对象现在继承RangedSummarizedExperiment(交易所)而不是分野。使用eSet的交易所API而不是(如colnames而不是sampleNames和化验而不是assayData)。包括annotatedDataFrameFrom Biobase-related所有内容已被删除。这意味着BigMatrix对象可以不再被添加到eSet / ExpressionSet GenoSet对象。1.21.10版本的变化- - - - - - - - - - - - - - - - - - - - - - - - - - - - o calcGC新特性被“基地”参数,处理“空空”前缀的存在与否更安全的方式。版本1.19.27变化- - - - - - - - - - - - - - - - - - - - - - - - - - - -新特性o rangeMeans数字na。rm参数,使用时间na少50%。rm = FALSE and少25%时间na.rm = TRUE。1.19.7版本的变化- - - - - - - - - - - - - - - - - - - - - - - - - o版本新特性介绍了rangeMeans家庭的功能,是IRanges密切相关:viewMeans家族的功能。这些新功能需要RleDataFrame和IRanges(或矩阵)的行范围和计算汇总统计。这些是很有用的摘要平均DNA拷贝数或覆盖的基因,通过样本。 These functions differ from view* in that they are more time efficient and they offer a 'simplify' argument to return a matrix, rather than a list. CHANGES IN VERSION 1.19.0 ------------------------- NEW FEATURES o This version introduces the RleDataFrame class. This class extends SimpleRleList and DataFrame. It stores a collection of like-length Rle objects. With the AtomicList features it behaves much like a matrix. For example, log2(x) - 1 works. We also have row and column sums and means. rangeSampleMeans functions like viewMeans. This object can be used to store runs of data along the genome for multiple samples, like coverage or DNA copy number. It can be used as an assayDataElement in a genoset (or any eSet). o segTable and segPairTable are dramatically faster. Stacking data.frames with segTable(RleDataFrame,stack=TRUE) argument is now instantaneous. DEPRECATED AND DEFUNCT o Previously we used a DataFrame for storing collections of Rle objects. This practice is now deprecated. Similarly, colMeans on a DataFrame is now deprecated. CHANGES IN VERSION 1.16.0 ------------------------- NEW FEATURES o cn2lr now has methods for vector, matrix, and DataFrame (of Rle) and allows you to center your log2ratio values on 2 copies, or on a specified 'ploidy' for your sample. o The BAFSet and CNSet classes have moved from deprecated to defunct. These classes only added getter/setter methods for baf/lrr/cn. Since these only cover some possible assayDataElements, it is better to use x[i,j,k], where k is the name of an assayDataElement. o All RangedData-related things have now progressed to defunct. Please use GRanges for locData and everywhere else. Since the genoset package provides a common API for GenoSet, GRanges, and RangedData, I hope this will be a simple change for everyone. o sampleNames and featureNames are now *un-deprecated*. Feel free to use them. They just call colnames and rownames, respectively. I have defined my own rownames and colnames functions. The eSet ones seem to do a lot of extra work, and the getter versions read from the first assayDataElement, rather than pData and fData. I changed to the latter, so BigMatrix assayDataElements will remain untouched until you really mean to access them.