Suggestions for example dataset

[PoisonAlien]

Hello @tkik @MaxSchoenung @HeyLifeHD @lutsik ,

As a part of the package it would be nicer to have an example data for testing/demonstration. Bsseq has BS.chr22 which can be loaded with the command data(BS.chr22). In methrix I included a part of single cell dataset from bsmap protocol - data(mm9_bsmap). However @tkik suggested that this dataset is quite "boring" and we should use something more robust - and I agree.

Two options:

1. We convert the dataset bundled with bsseq to methrix object and use it.
2. We make our own custom dataset from well studied in-house data.

If you opt for 2, we should make sure that we have at-lease two samples while keeping the object size small. For example, bsseq data is quite small (3.8MB) with ~50K loci and 2 samples. Bioconductor has a package size limit of 5 MB and the core team is quite strict in this regard.

> data(BS.chr22)
> BS.chr22
An object of type 'BSseq' with
  494728 methylation loci
  2 samples
has not been smoothed
All assays are in-memory
> print(object.size(x = BS.chr22), units = "MB")
3.8 Mb

Suggestions welcome, and please post here if you have an example set in mind.

[MaxSchoenung]

I am currently trying to generate some methrix “vanilla” dataset with hESC TET triple knockout. I will try this today and tell you how it works out tomorrow. If this is fine for you ;) Maximilian Schönung Cancer Epigenomics PhD Student

German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 280 69120 Heidelberg Germany phone: +49 6221 42-4321

m.schoenung@dkfz.demailto:m.schoenung@dkfz.de

On 28. May 2019, at 14:26, Anand Mayakonda notifications@github.com<mailto:notifications@github.com> wrote:

Hello @tkikhttps://github.com/tkik @MaxSchoenunghttps://github.com/MaxSchoenung @HeyLifeHDhttps://github.com/HeyLifeHD @lutsikhttps://github.com/lutsik ,

As a part of the package it would be nicer to have an example data for testing/demonstration. Bsseq has BS.chr22 which can be loaded with the command data(BS.chr22). In methrix I included a part of single cell dataset from bsmap protocol - data(mm9_bsmap). However @tkikhttps://github.com/tkik suggested that this dataset is quite "boring" and we should use something more robust - and I agree.

Two options:

1. We convert the dataset bundled with bsseq to methrix object and use it.
2. We make our own custom dataset from well studied in-house data.

If you opt for 2, we should make sure that we have at-lease two samples while keeping the object size small. For example, bsseq data is quite small (3.8MB) with ~50K loci and 2 samples. Bioconductor has a package size limit of 5 MBhttp://master.bioconductor.org/packages/devel/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#package-and-file-size-check and the core team is quite strict in this regard.

data(BS.chr22) BS.chr22 An object of type 'BSseq' with 494728 methylation loci 2 samples has not been smoothed All assays are in-memory print(object.size(x = BS.chr22), units = "MB") 3.8 Mb

Suggestions welcome, and please post here if you have an example set in mind.

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[PoisonAlien]

Yup! Sounds good to me :)