Entering edit mode

4.0 years ago

shrinka.genetics
▴
40

Hello I am working on WGBS data. I am using MethyKit package. I have created myobj as well as meth, but after that I got this error when doing clustering.

ClusterSamples(meth, dist= "correlation", method= "ward", plot=TRUE)

Error in ClusterSamples(meth, dist = "correlation", method = "ward", plot = TRUE) :

could not find function "ClusterSamples"

My question is there any other library needed to solve this? How can I solve it

Waiting for help

Regards

Shrinka Sen

Post Doctoral Fellow

BC Cancer Research

Vancouver

I used lower case only. Thanks

`library(methylKit)`

? Or you use a methylKit version in which the function has not been included yet. Try updating. Those are the possibilities you have.Thanks for your reply. How to update this?

Regards Shrinka

After doing this below mentioned error is showing, previously it was not there. I created myobj and with that did correlation plot. So now what to do? "NChr3-mod.txt", "KChr3-mod.txt", "CChr3-mod.txt", "EChr3-mod.txt", "PChr3-mod.txt") "SChr3-mod", "NChr3-mod", "KChr3-mod", "CChr3-mod", "EChr3-mod", "PChr3-mod"), assembly = "hg19", treatment = c(1,1,1,1,0,0,0,0), context = "CpG")

Error in data.table::fread(file = filepath, ...) :

Opened 168.6MB (176769180 bytes) file ok but could not memory map it. This is a 64bit process. There is probably not enough contiguous virtual memory available.

See the problem is not about the updated version of the package I think. The memory related issue what I mentioned in my last mail is not there if I use smaller file like below. Each

Chr3 file was >170000 KBwhereas each *Chr21 file is ~40000 KB. *Initially I used the command with Chr 3, now I ran it with Chr 21. Here I was able to create myobj "NChr21-mod.txt", "KChr21-mod.txt", "CChr21-mod.txt", "EChr21-mod.txt", "PChr21-mod.txt") "BChr21-mod", "SChr21-mod", "NChr21-mod", "KChr21-mod", "CChr21-mod", "EChr21-mod", "PChr21-mod"), assembly = "hg19", treatment = c(1,1,1,1,0,0,0,0), context = "CpG") uniting...Error in quantile.default(sds, sd.threshold) : missing values and NaN's not allowed if 'na.rm' is FALSETill there is the same issue. There is no NAs in the input files, I checked. Now how can I solve this?