Man pages for baumbachlab/keypathwayminer-R
KeyPathwayMiner R-Package

base64EncFileMethod for base64 encoding
call_kpm_localMethod for running KeyPathwayMineR localy
call_kpm_remoteMethod for running KeyPathwayMineR remotely
check_filesFunction which checks and processes files
check_parametersFunction which check parameters
combine_mutliple_matricesLogically combines multiple datasets
compute_z_scoresComputes z-score values of case samples
Configuration-classA configuration of the parameters K and L
create_indicator_from_fcurdleTestCreates indicator matrix from differentail
create_sca.SeuratConverts Seurat object to SingleCellAssay object
create_sca.SingleCellExperimentConverts SingleCellExperiment object to SingleCellAssay...
create_union_networkCreates a union network for the pathways of a specific...
dataset_listEncodes a list of datasets
determine_union_groupsDetermines from which pathways a node originates
do_diff_testing_via_MASTCalculates differentially expressed genes from single cell...
export_graphExport a graph
export_matrixSaves indicator matrix as a file.
export_nodesExport node ids
export_to_iGraphGet an iGraph object for a specific pathway
fetch_resultsOnce the run is complete, we can obtain the results
filter_fcHurdleTestResultsFilters the differential expression analysis results based on...
get_case_exceptionsCreates java arguments for case exceptions
get_configurationGet configuration object
get_configurationsGet all configuration names of a result
get_networksGet a data frame of available networks
get_pathwayGet specific pathway of a configuration
get_pathwaysGet all pathways for a specific configuration
get_resultsFetches result for remote run.
get_results_from_folderLoads results from folder with text files
get_result_urlReturns result url
get_startedFunctions which prints information on how to get started.
get_statusMethod to check up on a submitted job.
graph_kpmHelper method to encode custom network file
igraph_to_sifConverts igraph object to sif file.
import_graphReads graph file and converts it to igraph object
is_finishedCheck if asynchronous remote run is finished
kpmMain method used for running KPM
kpm_optionsSet or get options for KeyPathwayMineR
Pathway-classA pathway of a specific configuration.
pathway_comparison_plotsTwo pathway comparison plots.
pathway_statisticsComputes pathway statistics for all pathways in a result...
profile_pathwayRun gprofiler2's gost function on pathway of interesst
quest_progress_urlGet progress url
remove_configurationRemoves configuration from result object
reset_optionsResets kpm_options to default values
Result-classResult
ResultRemote-classResultRemote
retrieve_biogridRetrieves bioGRID network in suitable form for KPM
save_local_resultsSave results of the local run
save_remote_resultsSave results of the remote run
sc_to_indicator_matrixCalculates differentially expressed genes from single cell...
set_avg_expSet average differential expressed cases per gene
set_num_edgesSet number of edges given pathway object
set_num_nodesSet number of nodes given pathway object
set_pathwaySet pathway
setup_kpmSet up a JSON object in preparation of the job submission
sif_to_igraphConvert sif file to iGraph object
submit_kpmMethod for submitting a job to KeyPathwayMinerWeb Submits can...
test_jvmChecks the version of the JVM.
to_indicator_matrixConvertes numerical matrix to an indicator matrix
to_java_argumentsMethod which transform kpm_options() to java arguments.
visualize_resultShiny App for KeyPathwayMineR results
withTryCatchHelper method for error handling
baumbachlab/keypathwayminer-R documentation built on June 29, 2023, 11:21 a.m.