1.computeMatrix scale-regions -p 10 \ 2.-R gene19.bed geneX.bed \ 3.-S test1.bw test2.bw \ 4.-b 3000 -a 3000 \ 5.--regionBodyLength 5000 \ 6.--skipZeros \ 7.-o heatmap.gz reference-point mode则是给定一个bed file,以某个点为中心开始统计信号(TSS/TES/center)。但实际上我...
bigwigCompare computeMatrix 考虑到实际上bigwig是bam的另一种形式的存在,且函数运用和bam差不多,这里着重介绍一下bam文件的处理的几个函数: multiBamSummary bamCoverage bamCompare computeMatrix multiBamSummary 可以用来处理bam文件在基因组上覆盖情况,默认输出npz文件,衔接plotCorrelation和plotPCA进行作图。 有两种模...
Fly and mouse genes were scaled to different sizes due to the different median sizes of the two species' genes (genes ofD.melanogastercontain much fewer introns and are considerably shorter than mammalian genes). Thus, computeMatrix had to be run with slightly different parameters while the heatmap...
I already knew that " deeptools computeMatrix" can creat a matrix for plot.When I plot by plotProfile , I can not understand that what Y-axis means. Is it refers the score or the read counts of the bw files across per bin?? How " deeptoo...
1.computeMatrix scale-regions -p 10 \ 2.-R gene19.bed geneX.bed \ 3.-S test1.bw test2.bw \ 4.-b 3000 -a 3000 \ 5.--regionBodyLength 5000 \ 6.--skipZeros \ 7.-o heatmap.gz reference-point mode则是给定一个bed file,以某个点为中心开始统计信号(TSS/TES/center)。但实际上我...
hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args) 429 399 if args.sortRegions not in ['no', 'keep']: @@ -449,11 +419,3 @@ def main(args=None): 449 419 450 420 if args.outFileSorted...
(#813) * oops * fix testing and set a max number of filtered reads * apparently a bunch of things were getting skipped * fix wrappers * update computeMatrix wrapper * Decrease memory needs (#817) * Use an iterator to not blow memory up * Update a bit more * The GC bias stuff is ...
heatmapper: clustering parameters Please use the clustering only if you supplied just1 group of regionstocomputeMatrix. CommandExpected InputExplanation --kmeansINTEGERWhen this option is set, then the matrix is split into the number of indicated clusters using the kmeans algorithm. This willonlywork...
plotHeatmap does not change the values that computeMatrix calculated, it simply translates them into heatmaps and summary plots. It offers a large variety of parameters to explore various visualizations and customize the resulting image (see the commands above). In addition, you can retrieve all ...
computeMatrix 该功能可以计算每个基因区域的结合得分,生成中间文件用以给plotHeatmap和plotProfiles作图。 数据传递链 computeMatrix有两种模式,scale-regions mode和reference-point mode 区别展示图 scale-regiuons mode简单来说会将给定bed file范围内的结合信号做一个统计(指的是一段长度),并将基因长度统一scale到设定...