GenomicDataCommons

GenomicDataCommons copied to clipboard

size parameter in `manifest` not working

3

Hi Sean, @seandavi I can't really put my finger on it but recently the size parameter in the request is not working. For reprexample, ``` r suppressPackageStartupMessages({ library(GenomicDataCommons) }) files()...

LiNk-NY

Hi Sean, @seandavi It looks like query in the `somatic_mutations.Rmd` file would need to get updated to something like: ```r fnames = files() %>% GenomicDataCommons::filter( cases.project.project_id=='TCGA-SKCM' & data_format=='MAF' & data_type=='Annotated...

LiNk-NY

gdcdata should not depend on internet connection when cache=TRUE and you have all the files in your local cache

1

The GDC data download function `gdcdata` should not depend on an internet connection when `cache=TRUE` and it finds that you have all the files it needs in your local cache.

hermidalc

filter syntax for GDC query API "IS MISSING" and "NOT MISSING" operators

6

Sorry if I missed it in the docs or somewhere, but what is the `filter` syntax for GQL "missing" and "not missing"?

hermidalc

`GenomicDataCommons` is a very powerful library and can query pretty much anything at the GDC, though many users prefer other libraries like e.g.,`TCGAbiolinks` because the `GenomicDataCommons` query results data structure,...

hermidalc

gdc_rnaseq.R: gdc_rnaseq() on workflows other than "HTSeq - Counts" produce errors

2

sorry for raising two successive issues with this R script. i previously used the function to cache and return a SummarizedExperiment of HTSeq - Counts from TCGA data, and it...

lyijin

Apologies if I've missed where it is in the API, but I cannot find how to specify querying a previous GDC data release version.

hermidalc

This is a great package. However overwriting verbs without providing a default method means that loading this package after dplyr breaks dplyr. It doesn't need to. Just provide a default...

alanocallaghan

Doing so will require some significant refactoring, but having this option available might be useful....

seandavi

See https://docs.gdc.cancer.gov/API/Users_Guide/GraphQL_Examples/

seandavi