Re: [Bioc-devel] DataFrameList to Wide Format DataFrame
Hello,
Ah, yes, the sample names should of course be in the rows - Friday afternoon
error. In the question, I specified "largely the same set of features",
implying that the overlap is not complete. So, the example below will error.
DFL <- DataFrameList(X = DataFrame(a = 1:3, b = 3:1, row.names = LETTERS[1:3]),
Y = DataFrame(b = 4:6, c = 6:4, row.names =
LETTERS[20:22]))
unlist(DFL)
Error in .aggregate_and_align_all_colnames(all_colnames, strict.colnames =
strict.colnames) :
the DFrame objects to combine must have the same column names
This is long but works:
allFeatures <- unique(unlist(lapply(DFL, colnames)))
DFL <- lapply(DFL, function(DF)
{
missingFeatures <- setdiff(allFeatures, colnames(DF))
DF[missingFeatures] <- NA
DF
})
DFLflattened <- do.call(rbind, DFL)
Is there a one-line function for it?
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] DataFrameList to Wide Format DataFrame
A metadata column on a DataFrame runs along its 2nd dimension so is not a good place to put the list names. Have you tried unlist()? library(S4Vectors) DF <- DataFrame(id=letters[1:10], score=runif(10)) f <- sample(LETTERS[1:3], 10, replace=TRUE) DFL <- split(DF, f) DFL # SplitDataFrameList of length 3 # $A # DataFrame with 2 rows and 2 columns # id score # # 1 f 0.894709 # 2 h 0.801125 # # $B # DataFrame with 1 row and 2 columns # id score # # 1 d 0.538166 # # $C # DataFrame with 7 rows and 2 columns # id score # # 1 a 0.0145477 # 2 b 0.2507581 # 3 c 0.4388678 # 4 e 0.5219524 # 5 g 0.6377634 # 6 i 0.1892103 # 7 j 0.1829650 unlist(DFL) # DataFrame with 10 rows and 2 columns # id score # # A f 0.8947085 # A h 0.8011255 # B d 0.5381664 # C a 0.0145477 # C b 0.2507581 # C c 0.4388678 # C e 0.5219524 # C g 0.6377634 # C i 0.1892103 # C j 0.1829650 BTW this is a user question so is more appropriate for the support site. H. On 16/12/2021 22:00, Dario Strbenac via Bioc-devel wrote: Good day, Is there a function in the S4Vectors API which converts a DataFrameList into a DataFrame, automatically putting the list names into one of the metadata columns, analogous to MultiAssayExperiment's wideFormat function? The scenario is mutliple data sets from different organisations measuring the largely the same set of features and patient outcome, but on completely different sets of patients in each organisation. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] DataFrameList to Wide Format DataFrame
Good day, Is there a function in the S4Vectors API which converts a DataFrameList into a DataFrame, automatically putting the list names into one of the metadata columns, analogous to MultiAssayExperiment's wideFormat function? The scenario is mutliple data sets from different organisations measuring the largely the same set of features and patient outcome, but on completely different sets of patients in each organisation. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] BioC2022 Seattle July 27-29 hybrid conference organizing committee
Correction, I'd like to invite any interested members of the **community** to get involved! Feel free to get in touch with me with any questions. This is a great way to get to know other passionate Bioconductor users and developers while providing a great service to the community. On Thu, Dec 16, 2021 at 1:53 PM Levi Waldron wrote: > I'd like to invite any interested members of the committee to get involved > in organizing BioC2022, planned to be in a hybrid format in Seattle > July 27-29, 2022. There is lots to be done, including sponsorship and > funding, outreach, website, workshop technical organization, program > development, code of conduct communication and enforcement, and local > organization. Please fill out this form if you'd like to get involved: > https://forms.gle/cbjHww7uHJFRzwVx5 > > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BioC2022 Seattle July 27-29 hybrid conference organizing committee
I'd like to invite any interested members of the committee to get involved in organizing BioC2022, planned to be in a hybrid format in Seattle July 27-29, 2022. There is lots to be done, including sponsorship and funding, outreach, website, workshop technical organization, program development, code of conduct communication and enforcement, and local organization. Please fill out this form if you'd like to get involved: https://forms.gle/cbjHww7uHJFRzwVx5 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
