cbio.query {TRONCO} | R Documentation |
Wrapper for the CGDS package to query the Cbio portal. This can
work either automatically, if one sets cbio.study
,
cbio.dataset
or cbio.profile
, or interactively
otherwise. A list of genes to query with less than 900 entries should
be provided. This function returns a list with two dataframe: the
gentic profile required and clinical data for the Cbio study. Output
is also saved to disk as Rdata file. See also
http://www.cbioportal.org.
cbio.query( cbio.study = NA, cbio.dataset = NA, cbio.profile = NA, genes, file = NA )
cbio.study |
Cbio study ID |
cbio.dataset |
Cbio dataset ID |
cbio.profile |
Cbio genetic profile ID |
genes |
A list of < 900 genes to query |
file |
String containing filename for RData output. If NA no output will be provided |
A list with two dataframe: the gentic profile required and clinical data for the Cbio study.