"MethylKit" package for WGBS data

Question

[shrinka.genetics]

Hi

I am working with WGBS data, There I am using MethylKit package for DMC analysis. Differential DNA methylation is usually calculated by comparing the proportion of methylated Cs in a test sample relative to a control. In simple comparisons between such pairs of samples (i.e. test and control), methods such as Fisher’s exact test can be used. When there is only one sample per sample group, calculateDiffMeth() automatically applies Fisher’s exact test.

My question is as Fisher’s exact test has some limitations (DOI: 10.1093/nar/gku154), can Wald test be done using Methylkit?

Thanks
Shrinka

[viveksomya123]

I ran the annotateWithGeneParts() function in methylkit but I am getting below error. Kindly help.

List of command is as follow

library(genomation)
bed.file=system.file("extdata","refseq.hg18.bed.txt",package = "methylKit")
gene.parts=genomation::readTranscriptFeatures(bed.file)
genomation::annotateWithGeneParts(as(diffbin25p,"GRanges"),gene.obj)

genomation::annotateWithGeneParts(as(diffbin25p,"GRanges"),gene.obj)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'nearest': error in evaluating the argument 'x' in selecting a method for function 'ranges': subscript contains NAs
In addition: Warning messages:
1: In .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
2: In .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
3: In .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
4: In .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
5: In .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
6: In .merge_two_Seqinfo_objects(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

[Ram]

Why was this added as an answer to a 2 year old question? I'm moving it to a comment this time - please be more careful in the future.

[viveksomya123]

Why I am getting this histogram of CpG coverage using methylkit, is this the failure of bisulfite library preparation