Man pages for vitkl/MItools
Molecular interaction data tools, retrieving data using PSICQUIC service

benchmarkMotifsBenchmark linear motif instance found using QSLIMFinder...
benchmarkMotifsROCPlot ROC or precision-recall curves for motifs search...
browseMIontologybrowse Molecular Interaction ontology
centerDomainsCenter QSLIMFinder datasets (InteractionSubsetFASTA_list) at...
cleanMITAB'cleanMITAB' extracts interactor Uniprot (or other ID as...
cleanMITAB25'cleanMITAB' extracts and cleans a set of columns of MITAB2.5
cleanMITAB27'cleanMITAB' extracts and cleans a set of columns of MITAB2.7
collapseByInterProIDCollapse InterProScan output to one protein sequence feature...
domainEnrichmentdomainEnrichment: filter domains by background domain count...
domainProteinPairMatchCheck if the protein in the set2 is associated with domain...
downloadFastaDownload FASTA for a list of canonical (P04637) and isoform...
downloadFastaMixedDownload FASTA for a list of canonical (P04637) and isoform...
downloadFastaPostprocDownload FASTA for a list of post-processed chain ID (e.g....
edgelist2degreefind the degree for each protein given cleaned molecular...
edgelist2degreeFreqFind the degree distribution given edgelist (pair_id) and a...
ELMdb2GRangesDownload and read ELM database motif occurrences
extractInteractorsSubset MITAB to retrieve interactors, the number of...
filterBYmotifTypeFilter ELM database motif occurrence GRanges by motif type
filterInteractionSubsetFASTA_listFilter InteractionSubsetFASTA_list by the size of the...
findOverlapsBenchFind occuring GRanges overlapping with the benchmarking set...
foldEnrichment'foldEnrichment' calculates fold enrichment of a domain (or...
foldEnrichmentDistfind fold_enrichment distribution (in any domain or other...
foldEnrichmentPvalFind pvalue for each protein-feature pair in the network
fullInteractomeRetrieve interactome (proteins only or not) of a given...
GRangesINinteractionSubsetFASTACheck if proteins in GRanges were used for motif search using...
humanViralDegreeCompare viral and human protein degree distribution, filter...
interactionSubsetFASTAFASTA sequences of interactors of a specific protein
interactionSubsetMapIDinteraction_subset_from_2_sets renames ids in the...
interactorFeatureTypesdiscover types of interactor features in MITAB 2.7
interSpeciesInteractomeRetrieve interspecies interactions (proteins only or not) for...
lastIntActReleaselast IntAct (all IMEx databases) release
listInteractionSubsetFASTAget FASTA sequences of interactors of specific proteins: for...
listSingleInteractFromSet2Split interaction subset from 2 sets so that each elements...
loadAllIDProteinsload the list of all protein ID in UniProtKB
loadBioplexload Bioplex data
loadHumanViralPPIload human-human, human-viral and viral-viral PPI data from...
loadIntActFTPload all data from IntAct ftp
loadInterProTreeLoad the hierarchy of relationships between InterPro's...
loadMIontologyload Molecular Interaction ontology
loadTaxIDAllLowerload all lower taxonomy ID (all descendants)
loadTaxIDProteinsload the list of all proteins for given taxonomy ID (any...
merge2GRangesmcolsMerge data.table to GRanges metadata
MITABregionFeatureExtract binding region feature from cleaned MITAB2.7
motifVariantClassGenerate motif variant class (the first 2 element in the...
parReplicateparReplicate function from:...
permutationPvalcalculate permutation pval for association between X and Z if...
permutationPvalHelperfunctions that are called inside permutationPval
PermutResult2D2D bin plot of the features of top N domain-protein pairs as...
plotEnrichmentPlot the enrichment of domains that are likely to be...
PPInetwork2SLIMFinderFind linear motifs (QSLIMFinder or SLIMFinder) in the protein...
printMotifDomainTable'printMotifDomainTable' combines Domain enrichment and Motif...
QSLIMFinderCommandGenerate a QSLIMFinder command
queryPSICQUICUse PSICQUIC to query for molecular interactions (using MIQL,...
queryPSICQUICrlibdownload PSICQUIC query search result (only IMEx databases)...
randomGRangesGenerate random GRanges of equal length in the same sequence
randomInteractomeRetrieve molecular interactions for the random set of...
readInteractomeread Interactome into data.table
readInterProGFF3Read InterProScan output in the gff format, select sequence...
readQSLIMFinderMainRead and write QSLIMFinder results
recodeANDinteractionSubsetFASTARecode names and retrieve FASTA sequences of interactors of a...
recodeFASTARecode names of the AAStringSet object
reduceOverlappingGRangesReduce Overlapping GRanges keeping metadata (collapsing...
reduceWithMcolsReduce GRanges keeping metadata (collapsing withing each...
removeInteractionNoFASTARemove interactions if one participant doesn't have FASTA...
removeInteractionObsoleteIDRemove interactions if one participant has obsolete Uniprot...
removeSelfLoopsRemove self loops (self-interactions)
reorderMITAB25'reorderMITAB25' reorders interacting molecules in a pair...
reorderMITAB27'reorderMITAB27' reorders interacting molecules in a pair...
runCompariMotif3Run CompariMotif3
runQSLIMFinderRun a list of QSLIMFinder jobs
singleInteractFromSet2Filter interaction subset from 2 sets: keep only i-th element...
SLIMFinderOcc2GRangesRead QSLIMFinder (SLIMFinder) occurence output to Genomic...
subset2setsBy1IDSubset 2 sets of protein interaction data using a single ID...
subsetMITABbyIDRetrieve interactions for a list of interactors (given data...
subsetMITABbyMethodFilter molecular interactions by interaction detection...
subsetMITABbyPMIDsFilter molecular interactions by Pubmed ID
writeInteractionSubsetFASTA_listWrite InteractionSubsetFASTA_list into directory system...
XYZ.p.adjust'XYZ.p.adjust' adjusts p.value in the permutation result
vitkl/MItools documentation built on Jan. 12, 2018, 12:09 p.m.