2.23.1版更改---------------------- *在“DESeq”弃用后删除了对“CountDataSet”的强制方法。*更新小插图，以展示如何使用“EDASeq”与“DESeq2”。版本2.3的变化---------------------- *增加了函数getGeneLengthAndGCContent来计算基因长度和gc含量。*更新小插图。2.1版更改---------------------- *修复了plotPCA中的错误:参数k在SeqExpressionSet方法中没有正确传递。*修正了plotQuality中的错误:在相同的BAM/FASTQ文件中读取不同长度时进行修剪。2.0版的更改(主要更新)---------------------- * "exprs"和"exprs<-"现在已弃用:使用"counts"和"counts<-"来代替(为了与DESeq类兼容)。* "counts"现在访问原始计数(甚至在规范化之后)和"normCounts"访问规范化计数。*在SeqExpressionSet类中添加了槽位“normalizedCounts”:现在归一化函数将在这个新槽位中保存归一化计数，而在“counts”中保留原始计数。*在“MDPlot”中增加了选项，以红色显示控制基因。 * withinLaneNormalization and betweenLaneNormalization now always store the normalized counts in the normalizedCounts slot, even when offset=TRUE is used. * Added a new method plotPCA for Principal Components Analysis (PCA) plots. * Updated the vignette to reflect these changes. * DESCRIPTION and NAMESPACE cleaned up. Changes in Version 1.9 ----------------------- * Added method plotRLE for Relative Log Expression (RLE) plots. Changes in Version 1.3 ------------------------ * Fixed a bug in biasPlot relative to the lwd, xlab and ylab arguments. * Added a color_code option and changed the behavior of col in biasPlot. * Updated CITATION file. * Added an option to withinLaneNormalization and betweenLaneNormalization to return unrounded values. * A new way to deal with zero counts by adding a small positive constant. Changes in Version 1.2 ------------------------ * Fixed a bug in methods plotQuality and plotNtFrequency that now allow the strand information to be missing in the SAM/BAM file. * Fixed a bug in method biasPlot. It doesn't require anymore that one of the column of pData is called "conditions". * biasPlot method of SeqExpressionSet has now the argument "col" to specify the column of pData to use for color coding. Changes in Version 0.99.1 ------------------------ * The read-level EDA is now based on the classes BamFileList and FastqFileList of Rsamtools. The class ShortReadSet doesn't exist anymore. * Changed vignette Changes in Version 0.99.0 ------------------------ * Version number changed for submission to Bioconductor Changes in Version 0.0.6 ------------------------ * Fixed a bug in withinLaneNormalization to work with unnamed matrices * Fixed a bug in biasPlot to work with a single lane experiment * Added methods MDPlot and biasBoxplot * Changed the vignette and added an help page for newSeqExpression function Changes in Version 0.0.5 ------------------------ * Modified coerce from SeqExpressionSet to CountDataSet to treat the two class comparison in a separate way Changes in Version 0.0.4 ------------------------ * Added Vignette * Adjusted xlab in the boxplot method for signature FastqQuality * Changed getOffset and setOffset<- methods in offst and offst<- for compatibility with edgeR Changes in Version 0.0.3 ------------------------ * Added CITATION file * Added Help pages * Added data and extdata for the examples