#raggedexperiment

2017-05-14

Levi Waldron (22:02:29): > @Levi Waldron has joined the channel

Levi Waldron (22:02:29): > set the channel description: Discussion of the RaggedExperiment package

Marcel Ramos Pérez (22:02:29): > @Marcel Ramos Pérez has joined the channel

Martin Morgan (22:02:29): > @Martin Morgan has joined the channel

Levi Waldron (22:04:10): > Since there’s no issues tracker yet, I’m contributing here a small but full-featured dataset to help with demonstrating the package. It’s from on the TCGA ACC mutations dataset, subset to rownames found in the RPPA dataset.

Levi Waldron (22:05:04): > @Levi Waldronuploaded a file:ACCcolData.rdaand commented: Includes patient data and additional columns from the paper supplement, including subtypes. Could be trimmed. - File (Binary): ACCcolData.rda

Levi Waldron (22:05:19): > @Levi Waldronuploaded a file:ACCrowData.rdaand commented: Fromhttp://genomeportal.stanford.edu/pan-tcga/show_target_selection_file?filename=Allprotein.txt - File (Binary): ACCrowData.rda

Levi Waldron (22:05:43): > @Levi Waldronuploaded a file:ACCmutations.rdaand commented: The “Mutations” element fromhttp://s3.amazonaws.com/multiassayexperiments/accMAEO.rds - File (Binary): ACCmutations.rda

Levi Waldron (22:07:27): > The last object here is the RaggedExperiment object. I would have incorporated the rowData and colData into this, but noticed that the<-set method is not defined for rowData or colData of a RaggedExperiment (#issue, feature request).

Levi Waldron (22:19:58): > #issue Also the[[method doesn’t work, so I’m not sure how to extract a GRanges from the RaggedExperiment.

Levi Waldron (22:24:19): > #issue in the help page?RaggedExperiment, the “…” argument says “OR assay: Additional arguments for assay. See details for more information.” But there is no Details section.

Levi Waldron (22:25:46): > Hope you don’t mind me putting issues here for now since there isn’t an issue tracker yet for RaggedExperiment.

Unknown User (22:38:46): > @Levi Waldron commented on @Levi Waldron’s file https://community-bioc.slack.com/files/U34P8RS3B/F5CM38F4Y/accrowdata.rda: Actually, rowData doesn’t even make sense. Range metadata could be stored in the GRanges. - File (Binary): ACCrowData.rda

2017-05-15

Marcel Ramos Pérez (10:55:24): > @Levi WaldronThe package should be on GitHub athttps://github.com/Bioconductor/RaggedExperiment - Attachment (GitHub): Bioconductor/RaggedExperiment > Contribute to RaggedExperiment development by creating an account on GitHub.

Levi Waldron (10:57:48): > Oh, and with an issue tracker, thanks@Marcel Ramos Pérez!

Marcel Ramos Pérez (10:58:08): > Thank you!

Kasper D. Hansen (17:23:26): > @Kasper D. Hansen has joined the channel

2017-05-17

Marcel Ramos Pérez (14:08:57): > @Levi WaldronWe should go with providingRaggedExperiments as part of thecuratedTCGADatadatasets since they work well with theMultiAssayExperimentAPI.

Marcel Ramos Pérez (14:12:54): > Our argument for creatingRaggedExperimentstems from needing a matrix-like representation of ranges by samples. SupplyingGRangesLists would invalidate ourRaggedExperimentargument and forces us to adjust for this outside-of-the-API case.

Levi Waldron (14:47:17): > Agreed. In the S3 bucket perhaps they should just be tables, that are converted to RE by curatedTCGAData ()?

Marcel Ramos Pérez (15:29:44): > We’d have to port the functionality ofTCGAutilsfor that to be possible or publish that package andImportit

2017-05-19

Aedin Culhane (14:06:08): > @Aedin Culhane has joined the channel

2017-09-07

Michael Steinbaugh (07:20:30): > @Michael Steinbaugh has joined the channel

2017-10-27

Guangchuang Yu (06:44:27): > @Guangchuang Yu has joined the channel

2017-11-29

Matthew McCall (09:42:42): > @Matthew McCall has joined the channel

2018-04-20

Marcel Ramos Pérez (14:11:05): > Hi<!channel>, I’m archiving this channel. If there are any issues, feature requests, or questions, please post them on the support site or the github issues pagehttps://github.com/Bioconductor/RaggedExperiment/issues. - Attachment (GitHub): Bioconductor/RaggedExperiment > Contribute to RaggedExperiment development by creating an account on GitHub.

Marcel Ramos Pérez (14:11:26): > archived the channel