1.7.5版本的变化:主要/最新更新:quantifyCTSSs现在是一个通用的新的默认值。当进口权贵文件,瓷砖没有specifed瓷砖整个基因组的一个数字,而不是完全的大小。新的默认导入整个基因组是一个瓷砖。这应该是最快的选择对于小数据集,对于大型的数据集通常是更快的使用多个瓦片。——quantifyCTSSs现在接受bedGraph文件。与权贵进口,这在Windows中工作。-新转换*家庭之间的函数可以把ctss大佬/床/ bedGraph格式。——新checkCTSSs检查CTSSs-files是否正确格式化的,如果没有,希望输出一些有用的诊断。——新quickGenes集群级别的数据能够崩溃数据的包装器函数。检查装饰图案的用法的例子。 - New shapeMean function. - Many internal functions are now exposed as utils*-function. This should make it easier for power users and/or developers to modify and extend CAGEfightR. - Some internal changes to quantifyCTSSs and quantifyClusters for slightly better performance. - Fixed a small bug where assignGeneID counted NA as a gene when outputting a message. Note, this never affected the actual output of the function, just the message produced. CHANGES IN VERSION 1.5.3: - Added citation to BMC Bioinformatics paper. CHANGES IN VERSION 1.5: - Added new functions for spatial analysis of clusters: findLinks finds nearby pairs of clusters (for example TSSs and enhancers) and calculates the correlation of expression between them. findStretches find stretches along the genome where clusters are within a certain distance of eachother (for example groups of enhancer forming a super enhancer) and calculates the average pairwise correlation between members. - Changed the way clustering works: CAGEfightR uses coverage() to calculate genome-wide signals and now rounds the resulting signal to a certain number of digits (this can be modified via the CAGEfightR.round option), to prevent small positive or negative values due to floating point errors. This makes clustering more stable meaning the tuneTagClustering function is now deprecated. This should also increase the speed of most functions. - CAGEfightR now uses GPos instead of GRanges for storing CTSSs, this should result in improved memory performance. - Several changes to clusterBidirectionality: Balance is now calculated using the midpoint as well (preventing some rare cases where the midpoint could mask a single highly expressed CTSS), the pooled CTSS signal is now prefiltered for bidirectionality to increase speed and custom balance function can be provided (Bhattacharyya coefficient and Andersson's D are included). - Added new check-functions to make it easier to check if objects are formatted correctly CHANGES IN VERSION 0.99: - Submitted CAGEfightR to Bioconductor