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waldronlab / curatedTCGAData

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
https://bioconductor.org/packages/curatedTCGAData
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Viewing Clinical Data Floods Console With Text #13

Closed DarioS closed 1 year ago

DarioS commented 6 years ago

I am looking at clinical data for melanoma, but there's too much of it.

melanomaMicroRNA <- curatedTCGAData(diseaseCode = "SKCM", assays = "miRNASeqGene", dry.run = FALSE)
head(colData(melanomaMicroRNA))

Results in a lot of text being printed, ending with [ reached getOption("max.print") -- omitted 7 rows ].

Similarly, colnames(colData(melanomaMicroRNA)) ends with [ reached getOption("max.print") -- omitted 534 entries ].

Perhaps providing an option to just store some of the main clinical variables would make the table easier to work with.

lwaldron commented 6 years ago

I actually discussed this with @vjcitn recently - I think the gist of our conversation was that DataFrame itself could use a better show method for when there are lots of columns. In the meantime, you could identify the columns to the ones you most likely want with the getClinicalNames() function from waldronlab/TCGAutils repo, and subset the colData to only these.

LiNk-NY commented 1 year ago

This is more of an issue for S4Vectors::DataFrame..