Package: RGMQL 1.25.0
Simone Pallotta
RGMQL: GenoMetric Query Language for R/Bioconductor
This package brings the GenoMetric Query Language (GMQL) functionalities into the R environment. GMQL is a high-level, declarative language to manage heterogeneous genomic datasets for biomedical purposes, using simple queries to process genomic regions and their metadata and properties. GMQL adopts algorithms efficiently designed for big data using cloud-computing technologies (like Apache Hadoop and Spark) allowing GMQL to run on modern infrastructures, in order to achieve scalability and high performance. It allows to create, manipulate and extract genomic data from different data sources both locally and remotely. Our RGMQL functions allow complex queries and processing leveraging on the R idiomatic paradigm. The RGMQL package also provides a rich set of ancillary classes that allow sophisticated input/output management and sorting, such as: ASC, DESC, BAG, MIN, MAX, SUM, AVG, MEDIAN, STD, Q1, Q2, Q3 (and many others). Note that many RGMQL functions are not directly executed in R environment, but are deferred until real execution is issued.
Authors:
RGMQL_1.25.0.tar.gz
RGMQL_1.25.0.zip(r-4.5)RGMQL_1.25.0.zip(r-4.4)RGMQL_1.25.0.zip(r-4.3)
RGMQL_1.25.0.tgz(r-4.4-any)RGMQL_1.25.0.tgz(r-4.3-any)
RGMQL_1.25.0.tar.gz(r-4.5-noble)RGMQL_1.25.0.tar.gz(r-4.4-noble)
RGMQL_1.25.0.tgz(r-4.4-emscripten)RGMQL_1.25.0.tgz(r-4.3-emscripten)
RGMQL.pdf |RGMQL.html✨
RGMQL/json (API)
NEWS
| # Install 'RGMQL' in R: |
| install.packages('RGMQL', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:RGMQL-1.25.0(bioc 3.20)RGMQL-1.24.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:f7f3046f69
Exports:aggregateALLANYarrangeASCAVGBAGBAGDcollectcompile_querycompile_query_fromfilecondsCOUNTCOUNTSAMPcoverdelete_datasetDESCDGDGEDLDLEDOWNdownload_as_GRangesListdownload_datasetexecuteexport_gmqlextendfilterfilter_and_extractFULLgroup_byimport_gmqlinit_gmqllogin_gmqllogout_gmqlmapMAXMDMEDIANmergeMETAMINNILQ1Q2Q3read_gmqlread_GRangesListregister_gmqlremote_processingrun_queryrun_query_fromfilesample_metadatasample_regionsave_querysave_query_fromfileselectsemijoinsetdiffshow_all_metadatashow_datasets_listshow_job_logshow_jobs_listshow_queries_listshow_samples_listshow_schemaSQRTSTDstop_gmqlstop_jobSUMtaketrace_jobunionUPupload_dataset
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurldata.tableDelayedArraydplyrfansiformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyrR6RcppRCurlrestfulrRGMQLlibRhtslibrJavarjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrswithrXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Method aggregate | aggregate aggregate,GMQLDataset-method aggregate-method |
| AGGREGATES object class constructor | AGGREGATES-Object AVG BAG BAGD COUNT COUNTSAMP MAX MEDIAN MIN Q1 Q2 Q3 STD SUM |
| Method arrange | arrange arrange,GMQLDataset-method arrange-method |
| Method collect | collect collect,GMQLDataset-method collect-method |
| Compile GMQL query | compile_query compile_query_fromfile |
| Method cover | cover cover,GMQLDataset-method cover-method |
| PARAM object class constructor | ALL ANY Cover-Param |
| Delete dataset | delete_dataset |
| DISTAL object class constructor | DG DGE DISTAL-Object DL DLE DOWN MD UP |
| Download Dataset | download_as_GRangesList download_dataset |
| Condition evaluation functions | condition_evaluation conds Evaluation-Function |
| GMQL Function: EXECUTE | execute |
| Create GMQL dataset from GRangesList | export_gmql |
| Method extend | extend extend,GMQLDataset-method extend-method |
| Method filter | filter filter,GMQLDataset-method filter-method |
| Filter and extract function | filter_and_extract |
| PARAM object class constructor | filter-extract FULL |
| Method group_by | group_by group_by,GMQLDataset-method group_by-method |
| Create GRangesList from GMQL dataset | import_gmql |
| Init GMQL server | init_gmql |
| Show a job log or trace | log_job show_job_log trace_job |
| Login to GMQL | login_gmql |
| Logout from GMQL | logout_gmql |
| Method map | map map,GMQLDataset-method map-method |
| Method merge | merge merge,GMQLDataset,GMQLDataset-method merge-method |
| OPERATOR object class constructor | META NIL OPERATOR-Object SQRT |
| Ordering functions | ASC DESC Ordering-Functions |
| Function read | read_gmql read_GRangesList |
| Register into remote GMQL | register_gmql |
| Disable or Enable remote processing | remote_processing |
| Run a GMQL query | run_query run_query_fromfile |
| Show metadata list from dataset sample | sample_metadata |
| Show regions data from a dataset sample | sample_region |
| Save GMQL query | save_query save_query_fromfile |
| Method select | select select,GMQLDataset-method select-method |
| Semijoin condition | semijoin |
| Method setdiff | setdiff setdiff,GMQLDataset,GMQLDataset-method setdiff-method |
| Show a metadata cartesian product of all metadata present into the dataset and the region sets | show_all_metadata |
| Show datasets | show_datasets_list |
| Show all jobs | show_jobs_list |
| Show all queries | show_queries_list |
| Show dataset samples | show_samples_list |
| Show dataset schema | show_schema |
| Stop GMQL server | stop_gmql |
| Stop a job | stop_job |
| Method take | take take,GMQLDataset-method take-method |
| Method union | union union,GMQLDataset,GMQLDataset-method union-method |
| Upload dataset | upload_dataset |
