1.7.5版本的变化:- MAJOR/BREAKING UPDATE: quantifyCTSSs现在是一个泛型，有新的默认值。在导入BigWig文件时，tile没有指定为整个基因组中的单个tile数量，而是以碱基对为单位。新的默认设置是将整个基因组作为单个瓦导入。对于小型数据集，这应该是最快的选择，对于较大的数据集，使用多个块通常更快。quantifyCTSSs现在接受床图文件。与BigWig导入不同，这适用于Windows。-新的convert*系列函数，可以在BigWig/BED/bedGraph格式之间转换CTSSs。-新的checkctss检查ctss文件是否正确格式化，如果不是，将有望输出一些有用的诊断。-新的quickGenes包装器功能，用于将集群级数据折叠为基因级数据。检查小插图的用法示例。 - 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