Sesame Data cache HM450

[YuanningEric]

Hi,

I am using the SesameData package to retrieve the manifest for the HM450 array as a GRange object ("EH3675"). However, I was not able to cache the file using the command sesameDataCache("HM450"). I was able to get the manifest for the HM27 and EPIC arrays. The package version I am using is SesameData 1.12.0.

Could you please check what happens?

[zwdzwd]

Hi Eric, can you retrieve by EH number directly? like ExperimentHub()[['EH3675']]? It might be because the cache table is missing this file. Since there are more Illumina arrays that are emerging, we planning to retire the sesameDataCache(platform) but have it cache all sesameData in the future. I see that you are developing a new package. Maybe you would want to try the development version of sesameData since we do have some update (largely based on request from a recent Bioconductor review). Hope this is helpful.

[zwdzwd]

To be specific, https://github.com/zwdzwd/sesameData/blob/master/R/manifest.R we have an exported function that gives you GRanges manifest now.

[YuanningEric]

Hi Wanding,

Thanks for your answer. ! Yes, I can retrieve the annotation by EH number directly.

[tiagochst]

@zwdzwd This function is not retrieving for hg19.

[zwdzwd]

@tiagochst yeah, we are likely not going to continue supporting hg19. But you can always get the hg19 manifest using the older EH numbers. Sorry about the inconvenience.

>eh = query(ExperimentHub(),"sesameData")
>eh[grepl("HM450.hg19.manifest", eh$title)]
ExperimentHub with 3 records
# snapshotDate(): 2022-03-16
           title
  EH1423 | HM450.hg19.manifest
  EH1679 | HM450.hg19.manifest
  EH3674 | HM450.hg19.manifest

>eh[['EH3674']]
GRanges object with 485577 ranges and 52 metadata columns:
             seqnames      ranges strand | address_A address_B     channel
                <Rle>   <IRanges>  <Rle> | <integer> <integer> <character>
  cg13869341     chr1 15865-15866      - |  62703328  16661461         Red
  cg14008030     chr1 18827-18828      - |  27651330      <NA>        Both
  cg12045430     chr1 29407-29408      - |  25703424  34666387         Red
  cg20826792     chr1 29425-29426      - |  61731400  14693326         Red
  cg00381604     chr1 29435-29436      - |  26752380  50693408         Red
         ...      ...         ...    ... .       ...       ...         ...
  cg05001044     chrM   6762-6763      - |  61635473      <NA>        Both
  cg03344490     chrM   6798-6799      + |  11637485      <NA>        Both
  cg18024856     chrM   7197-7198      - |  47665304  25788501         Red
  cg03348902     chrM   9055-9056      + |  31704508      <NA>        Both
  cg01070250     chrM   9139-9140      + |  17682330      <NA>        Both

[tiagochst]

No problem! Thank you for letting me know. I already updated my package using the EH numbers.

On Thu, Mar 24, 2022 at 5:49 PM Wanding Zhou - Bioinformatics < @.***> wrote:

@tiagochst https://github.com/tiagochst yeah, we are likely not going to continue supporting hg19. But you can always get the hg19 manifest using the older EH numbers. Sorry about the inconvenience.

eh[grepl("HM450.hg19.manifest", eh$title)] ExperimentHub with 3 records

snapshotDate(): 2022-03-16

       title

EH1423 | HM450.hg19.manifest EH1679 | HM450.hg19.manifest EH3674 | HM450.hg19.manifest

eh[['EH3674']] GRanges object with 485577 ranges and 52 metadata columns: seqnames ranges strand | address_A address_B channel <Rle> <IRanges> <Rle> | cg13869341 chr1 15865-15866 - | 62703328 16661461 Red cg14008030 chr1 18827-18828 - | 27651330 <NA> Both cg12045430 chr1 29407-29408 - | 25703424 34666387 Red cg20826792 chr1 29425-29426 - | 61731400 14693326 Red cg00381604 chr1 29435-29436 - | 26752380 50693408 Red ... ... ... ... . ... ... ... cg05001044 chrM 6762-6763 - | 61635473 <NA> Both cg03344490 chrM 6798-6799 + | 11637485 <NA> Both cg18024856 chrM 7197-7198 - | 47665304 25788501 Red cg03348902 chrM 9055-9056 + | 31704508 <NA> Both cg01070250 chrM 9139-9140 + | 17682330 <NA> Both

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