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transmart2cbio.mapping.txt
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#tranSMART to cBioPortal clinical mapping file
#comments start with #
#cbioportal
#path to the directory to create
target path=
#meta study
study id=
study name=
study short name=
study description=
#short name of the type e.g. BRCA (note ALL CAPS) for breast cancer
study type=
#optional
study citation=
#optional, pubmedid
study pmid=
#type of cancer, optional unless defining a new type of cancer
type name=
type short=
type keywords=
type color=
type short name=
#import script
importer command=$PORTAL_HOME/core/src/main/scripts/cbioportalImporter.py --jvm-args "-cp $CONNECTOR_JAR:$PORTAL_HOME/core/target/core-1.0-SNAPSHOT.jar" --command
importer remove old study=TRUE
#meta clinical
#path to the source clinical data file
clinical file path=
#clinical mapping of special attributes, specify concept path in tranSMART, remove quotes and use forward slashes (/)
#cbioportal expects years
clinical mapping AGE path=
#days2years, days2months, months2years, months2days, years2months, years2days
clinical mapping AGE convert=
clinical mapping SEX path=
#regex replace, specify a regular expression and what should it be substituted with, separated by TAB, there can be multiple
clinical mapping SEX replace=1 MALE
clinical mapping SEX replace=0 FEMALE
#cbioportal doesn't do anything special with this column yet and doesn't expect particular values
clinical mapping RACE path=
#cbioportal doesn't do anything special with this column yet and doesn't expect particular values
clinical mapping ETHNICITY path=
#cbioportal expects years
clinical mapping AGE_AT_DIAGNOSIS path=
clinical mapping TUMOR_TYPE path=
clinical mapping DAYS_TO_DEATH path=
clinical mapping DAYS_TO_DEATH convert=
clinical mapping OS_STATUS path=
clinical mapping OS_STATUS replace=1 LIVING
clinical mapping OS_STATUS replace=0 DECEASED
clinical mapping OS_MONTHS path=
clinical mapping OS_MONTHS convert=
clinical mapping DFS_STATUS path=
clinical mapping DFS_STATUS replace=
clinical mapping DFS_MONTHS path=
clinical mapping DFS_MONTHS convert=
clinical mapping CANCER_TYPE path=
clinical mapping TUMOR_SITE path=
#regex replace on concepts path - allows customization of column names, specify a regular expression and what should it be substituted with, separated by TAB
clinical mapping concept to column name replace=
#specify a column name for a specific concept, for example "clinical mapping type \Characteristics\DrugA = DrugAResponse"
clinical mapping type <custom concept> =
#meta expression
expression file path=
#one of VALUE, LOG2E or ZSCORE
expression data column=
#by default study name + Expression data
expression profile name=
#by default study name + Expression data
expression profile description=
#one of FIRST, LAST, AVERAGE, GEOMETRICAVERAGE or ERROR (default)
expression aggregate=
#column name for Entrez gene id, by default GENE ID
expression entrez column=
#column name for Hugo gene symbol, by default GENE SYMBOL
expression hugo column=
#meta copy number
copynumber file path=
#by default FLAG
copynumber data column=
#by default study name + Copy number data
copynumber profile name=
#by default study name + Copy number data
copynumber profile description=
#meta segmented copy number
segmented file path=
#by default study name + segmented copy number data
segmented profile name=
#by default study name + segmented copy number data
segmented profile description=
#by default FLAG
segmented data column=