Problem with the tile_by_windows() function

[marin-e]

Hi,

I am using MethylSig v1.0.0 on RRBS data. I have a problem with the tile_by_windows() function. I ran tile_by_windows() on this bsseq object :

bs
An object of type 'BSseq' with
  7194960 methylation loci
  9 samples
has not been smoothed
All assays are in-memory

Then I applied:

windowed_bs <- tile_by_windows(bs = bs, win_size = 25)

And I obtained the following bsseq object:

windowed_bs
An object of type 'BSseq' with
  123890520 methylation loci
  9 samples
has not been smoothed
All assays are in-memory

I don't understand why I have more methylation loci after tilling than before.

Do you have an explanation?

Thank you

[rcavalcante]

Hi,

Please see #47 (comment). Summarizing the salient point:

I usually do the following order of calls:

1. bsseq::read.bismark()
2. tile_by_windows()
3. filter_loci_by_coverage()
4. filter_loci_by_group_coverage()
5. diff_methylsig()

All those extra loci are regions with no signal in them. The tiling function is a little "dumb" in the sense that it doesn't filter out non-zero regions for you, so you should run filter_loci_by_group_coverage() after tiling.

Raymond

[marin-e]

Hi,

Thank you for the clarification (sorry, I didn't realize that the topic was the same that #47).

Marine

[rcavalcante]

No problem, I'll go ahead and close the issue. Have a nice day.