WGBS Data Analysis Related

Question

[shrinka.genetics]

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

Answer 1

[ATpoint]

Lowercase c => clusterSamples

[shrinka.genetics]

I used lower case only. Thanks

[ATpoint]

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.

[shrinka.genetics]

Thanks for your reply. How to update this?

Regards Shrinka

[ATpoint]

BiocManager::install("methylKit")

[shrinka.genetics]

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.

[shrinka.genetics]

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 KB whereas 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 FALSE

Till there is the same issue. There is no NAs in the input files, I checked. Now how can I solve this?