Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
harmonize.r now calls process.duplicate.genes.2 for handling gene roll up.
Changed data.matrix function in harmonize.r to data.matrix.harmonize to avoid conflict with base function called in pgdac_ptmsea_functions.R
harmonize.r now checks if pome.duplicate.gene.policy exists. If it does not, the script creates that variable and sets it to the duplicate.gene.policy variable value (which by default is set to maxvar)
harmonize.r checks if policy is SGT. If it is, the script then adds subgroupNum to the rdesc columns
process_duplicate_genes.r calls process.duplicate.genes (the original one) from within process.duplciate.genes.2 if policy is either mean, maxvar, or median.
Other Changes:
setup.sh now adds latest tag to every docker that gets built along with the original commit hash tag. To clarify, every docker that gets built will have two tags:
most recent six-character git commit hash
latest
setup.sh pushes both the tags to Dockerhub
There will be only one latest tag for each docker_namespace/docker_name and will point to the most recent docker added to Dockerhub
All Dockerfiles and WDLs now have broadcptacdev/docker_name:latest for docker references
update.shNO longer has the code that:
interacts with the docker API to get the most recent docker tag for each parent docker
updates child Dockerfile with the retrieved most-recent tag for its parent docker
update.sh no longer builds and pushes the docker whose children need to be updated
harmonize.rnow callsprocess.duplicate.genes.2for handling gene roll up.data.matrixfunction inharmonize.rtodata.matrix.harmonizeto avoid conflict with base function called inpgdac_ptmsea_functions.Rharmonize.rnow checks ifpome.duplicate.gene.policyexists. If it does not, the script creates that variable and sets it to theduplicate.gene.policyvariable value (which by default is set tomaxvar)harmonize.rchecks if policy is SGT. If it is, the script then adds subgroupNum to therdesccolumnsprocess_duplicate_genes.rcallsprocess.duplicate.genes(the original one) from withinprocess.duplciate.genes.2if policy is eithermean,maxvar, ormedian.Other Changes:
setup.shnow adds latest tag to every docker that gets built along with the original commit hash tag. To clarify, every docker that gets built will have two tags:setup.shpushes both the tags to Dockerhubdocker_namespace/docker_nameand will point to the most recent docker added to Dockerhubbroadcptacdev/docker_name:latestfor docker referencesupdate.shNO longer has the code that:update.shno longer builds and pushes the docker whose children need to be updated