cBioPortalData

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Possible mistake in .isNonExp function causes files (CNA etc) to be loaded as metadata?

4

Hello, I was loading a study using the function `loadStudy` and noticed that most data files are not being added to the `ExperimentList` of the `MultiAssayExperiment` object, but are loaded...

SRodenburg

pancan_pcawg_2020 and pan_origimed_2020

4

Hi Waldron Lab, I'm working on migrating my cBioPortal workflow code to use cBioPortalData, and the package is really excellent. Great work. One thing that I've noticed is that `pancan_pcawg_2020`...

mjsteinbaugh

add unit tests to match calls between direct API and cached API calls

LiNk-NY

brca_tcga_pan_can_atlas_2018 is failing with `cBioDataPack`

11

Hi, I'm seeing a parsing error for `brca_tcga_pan_can_atlas_2018`: `utils::read.table` chokes too easily on malformed files -- is it worth considering switching to readr/vroom or data.table here to harden against malformed...

mjsteinbaugh

loadStudy error

1

@LiNk-NY I have an issue when trying to load the data. The issue seems to be with the data_sv. txt/ Where we have multiple clumns `Site_1_Chromosome`, `Site_2_Chromosome` etc. Probably, not...

gadepallivs

I noticed an issue when trying to wrap the `cBioPortalData()` function within another function or the `mapply()` function. It seems that when multiple arguments to `cBioPortalData()` are being passed in...

krlong68

Error in `.checkFixSampleMap(sampleMap)`

1

Hi! I'm getting the below error for my query: ``` > cbio_api study samples cBioPortalData( + api = cbio_api, + by = "hugoGeneSymbol", + studyId = study, + sampleIds =...

shbrief

Not time-critical, but there are 115 NA values in the `getStudies(cbio, buildReport = TRUE)` api_build and pack_build columns. I'm guessing these are studies added to cBioPortal since the last time...

lwaldron