I'm hoping someone has experience using the BiSeq package in R. I'm going through the "An Introduction to BiSeq" pdf available at the following website:

So far I have successfully imported my data into R using the readBismark command suggested in the tutorial. I have been able to work through sections 2 and 3 without error. However, when I get to section 4.1, definition of CpG clusters, I run into an error. I am using the same code they do, but changing $group to $treatment, as that is what my column in colData is named. Below is the code, and resulting error.

rrbs.clust<-clusterSites(object=rrbs,groups=colData(rrbs)$treatment,perc.samples=4/5,min.sites=20,mx.dist=100)

Error in .filterBySharedRegions_BSraw(object, groups, perc.samples, minCov = 1) :

Length of no.samples should be 1 or the same as the number of group levels.

There seems to be an issue with the no.samples, but I'm not familiar enough with R to figure out how to fix the problem. Any help would be appreciated. Thank you very much!

So far I have successfully imported my data into R using the readBismark command suggested in the tutorial. I have been able to work through sections 2 and 3 without error. However, when I get to section 4.1, definition of CpG clusters, I run into an error. I am using the same code they do, but changing $group to $treatment, as that is what my column in colData is named. Below is the code, and resulting error.

rrbs.clust<-clusterSites(object=rrbs,groups=colData(rrbs)$treatment,perc.samples=4/5,min.sites=20,mx.dist=100)

Error in .filterBySharedRegions_BSraw(object, groups, perc.samples, minCov = 1) :

Length of no.samples should be 1 or the same as the number of group levels.

There seems to be an issue with the no.samples, but I'm not familiar enough with R to figure out how to fix the problem. Any help would be appreciated. Thank you very much!

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