search

genomicsclass / labs

Rmd source files for the HarvardX series PH525x
http://genomicsclass.github.io/book
MIT License
2.01k stars 1.95k forks source link

Updating eset_sumexp.Rmd to modern syntax. #84

Closed gillsignals closed 5 years ago

gillsignals commented 5 years ago

This PR addresses syntax changes affecting the SummarizedExperiment class in eset_sumexp.Rmd. rowRanges replaces rowData and metadata replaces exptData. Comments are also added to help students follow along.

Also modified the .gitignore to cover .Rproj.user files.

Thanks!

vjcitn commented 5 years ago

On Fri, Oct 25, 2019 at 6:33 PM gillsignals notifications@github.com wrote:

@gillsignals commented on this pull request.

In bioc/eset_sumexp.Rmd https://github.com/genomicsclass/labs/pull/84#discussion_r339260718:

ExpressionSet


-dim(e)
+# exprs gives expression matrix
+dim(e)    # number of features and samples in ExpressionSet
 exprs(e)[1:3,1:3]

Are you referring to line 27, which was unchanged in my previous commit? I
am happy to change that if you want, but that is the format in the textbook
and how it is shown in the course. Having said that, there are many places
in the Rmds where this would need to be changed if we choose to do that.

Would you like that done?

I would say this is a low priority. If it seems useful to query students on appreciation of the differences then let's use the concept in a problem. Otherwise ignore the comment. I will merge the PR.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/genomicsclass/labs/pull/84?email_source=notifications&email_token=ABDI5QVSKCF7SK5SICMLD2DQQNX3LA5CNFSM4JFEXQQKYY3PNVWWK3TUL52HS4DFWFIHK3DMKJSXC5LFON2FEZLWNFSXPKTDN5WW2ZLOORPWSZGOCJJ4NIY#discussion_r339260718, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDI5QXX7AWFBOKYFQYCKZLQQNX3LANCNFSM4JFEXQQA .

-- The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance  HelpLine at http://www.partners.org/complianceline http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.