NEWS.md
cgdsr
to cBioPortalData
migration vignette (@kmezhoud, #54)cBioDataPack
api. = api/v2/api-docs
in cBioPortal
to access the API protocol’s new locationfetchData
developer function added to handle both molecularData
and mutationData
requests as deduced from the molecularProfileIds
vectortoken
string or file can now be included in the cBioPortal
function.check_build
argument can be set to FALSE
for alternative APIs, e.g., KidsFirst, when using cBioPortalData
queryGeneTable
translates gene IDs (‘hugoGeneSymbols’ <> ‘entrezGeneIds’) via the API servicegetDataByGenes
supersedes getDataByGenePanel
getStudies()
replaces data('studiesTable')
to discover study IDsgetStudies()
, which has replaced data('studiesTable')
.cBioDataPack
.cBioPortalData
checks the data(studiesTable)
to verify that study datasets are building, otherwise provide a message in interactive sessions.getDataByGenePanel
deprecated for getDataByGenes
which handles input of both gene panels and genescBioPortalData
now allows for gene inputs as either Entrez IDs or Hugo symbols (#24, @jucor) and sampleIds
inputgene
inputs are provided, the by
argument has to agree with the type of genes provided (either be entrezGeneId
or hugoGeneSymbol
).metadata
from cBioDataPack
were missing (‘LICENSE’ and ‘Fusion’; #37)loadStudy
allows cleanup=TRUE
for removing files after untar
-ingcitation("cBioPortalData")
studiesTable
includes additional columns pack_build
and api_build
to indicate to the user which datasets have been successfully built as MultiAssayExperiment
objects. Users will be notified when a dataset, reported as not building, is requested from the cBioDataPack
function.sampleIds
argument to getDataByGenePanel
as part of cache re-workcBioPortal
(@inodb, #16)cBioDataPack
downloads from a more robust repository (AWS S3; @inodb, #22)removePackCache
and removeDataCache
now remove data from the user’s cache based on inputs to respective functions (cBioDataPack
and cBioPortalData
)cBioDataPack
.read.delim
instead of read_tsv
internally to avoid assigning NA
to chromosome columntestthat
cBioDataPack
and cBioPortalData
in the documentationgeneTable
function (@xinwei-sher, #29)cBioDataPack
allows users to download packaged data objects from download.cbioportal.org/BiocFileCache
to avoid re-downloadingcBioPortalData
lets users query the cbioportal.org API and retrieve slices of data according to gene, molecular profile identifiers, etc.cBioPortalData
use a caching mechanism to avoid repeat downloads of data and improve load timesMultiAssayExperiment
as the primary data representationAnVIL
package which makes use of rapiclient
to provide an automatic R interface to the API