为什么DiffBand分析所得的差异peaks长度都是401?这个问题一直没找到答案,跟别人的帖子跑的,发现教程的例子peaks的长度不是固定的,找了一些发表的文章中的附表,peaks的长度也是不固定的,那说明我跑的代码是有问题的,肯定有参数没设置对,但一直没找到帖子有说这个问题,幸得同学提醒,去看了下DiffBand的说明书,终于找到了问题的原因所在。
在RStudio中查询了dba.count()命令的参数,其中对于summits有如下描述:
unless set to FALSE, summit heights (read pileup) and locations will be calculated for each peak. The values can retrieved using dba.peakset. The summits can also be used as a read score in the global binding matrix (see score).
If the value of summits is TRUE (or 0), the summits will be calculated but the peaksets will be unaffected. If the value is greater than zero, all consensus peaks will be re-centered around a consensus summit, with the value of summits indicating how many base pairs to include upstream and downstream of the summit (so all consensus peaks will be of the same width, namely 2 * summits + 1).
也就是说dba.count()默认参数设置了summits=200,width=2 * summits + 1,即401。要解决这个问题,得把参数summits=200改为summits=FALSE,就可以解决这一问题,得到的差异peaks长度不是固定值了。