Package index • MolEvolvR

All functions

GCA2Lineage(): Function to map GCA_ID to TaxID, and TaxID to Lineage

IPG2Lineage(): IPG2Lineage

summarizeByLineage() summarizeDomArch_ByLineage() summarizeDomArch() summarizeGenContext_ByDomArchLineage() summarizeGenContext_ByLineage() summarizeGenContext() totalGenContextOrDomArchCounts(): MolEvolvR Summary

acc2FA(): acc2FA

acc2Lineage(): acc2Lineage

addLeaves2Alignment(): addLeaves2Alignment

addLineage(): addLineage

addName(): addName

addTaxID(): addTaxID

alignFasta(): alignFasta

assignJobQueue(): assignJobQueue

calculateEstimatedWallTimeFromOpts(): calculateEstimatedWallTimeFromOpts

calculateProcessRuntime(): calculateProcessRuntime

cleanClusterFile(): Clean Cluster File

cleanClusters(): Cleanup Clust

cleanDomainArchitecture(): Cleanup DomArch

cleanFAHeaders(): Cleanup FASTA Header

cleanGeneDescription(): Cleanup GeneDesc

cleanGenomicContext(): Cleanup Genomic Contexts

cleanLineage(): Cleanup Lineage

cleanSpecies(): Cleanup Species

cleanString(): Clean String

combineFiles(): Download the combined assembly summaries of genbank and refseq

combineFullAnalysis(): Combining full_analysis files

combineIPR(): Combining clean ipr files

condenseRepeatedDomains(): condenseRepeatedDomains

convert2TitleCase() to_titlecase(): Changing case to 'Title Case'

convertAlignment2FA(): convertAlignment2FA

convertAlignment2Trees(): convertAlignment2Trees

convertFA2Tree(): convertFA2Tree

convertIPRScanDomainTable2FA(): Using the table returned from createIPRScanDomainTable, construct a domain fasta for a single accession number in the original fasta (i.e., the original fasta argument to createIPRScanDomainTable())

countByColumn(): countByColumn

createBinaryDomainNetwork(): Domain Network

createDomainNetwork(): Domain Network

createFA2Tree(): createFA2Tree

createGenomicContextNetwork(): Genomic Context Directed Network

createIPRScanDomainTable(): For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file

createJobResultsURL(): Given a pin_id, returns the URL where the user can check the status of their job

createJobStatusEmailMessage(): Produces a mail message that can be sent to a user when their job is accepted. Used by the sendJobStatusEmail() method.

createLineageLookup(): createLineageLookup

createMSA_Kalign(): Function to generate MSA using kalign

createMSA_PDF(): Multiple Sequence Alignment

createRepresentativeAccNum(): createRepresentativeAccNum

createUndirectedGenomicContextNetwork(): createUndirectedGenomicContextNetwork

createWordCloud2Element(): Wordclouds for the predominant domains, domain architectures.

createWordCloudElement(): Wordclouds for the predominant domains, domain architectures

downloadAssemblySummary(): Download the combined assembly summaries of genbank and refseq

efetchIPG(): efetchIPG

elements2Words(): elements2Words

ensureUniqAccNum(): make accnums unique

extractAccNum(): extractAccNum

filterByDomains(): filterByDomains

filterByFrequency(): filterByFrequency

findParalogs(): findParalogs

formatJobArgumentsHTML(): Format job arguments into html-formatted key/value pairs, for including in an email

generateAllAlignments2FA(): generateAllAlignments2FA

getAccNumFromFA(): getAccNumFromFA

getDomainsFromFA(): getDomainsFromFA

getIPRScanColNames(): Constructor function for interproscan column names (based upon the global variable written in molevol_scripts/R/colnames_molevol.R)

getIPRScanColTypes(): construct column types for reading interproscan output TSVs (based upon the global variable written in molevol_scripts/R/colnames_molevol.R)

getProcessRuntimeWeights(): getProcessRuntimeWeights

getTopAccByLinDomArch(): getTopAccByLinDomArch

mapAcc2Name(): mapAcc2Name

mapAdvOption2Process(): mapAdvOption2Process

mapOption2Process(): mapOption2Process

plotEstimatedWallTimes(): plotEstimatedWallTimes

plotIPR2Viz(): plotIPR2Viz

plotIPR2VizWeb(): plotIPR2VizWeb

plotLineageDA(): Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages

plotLineageDomainRepeats(): Lineage Domain Repeats Plot

plotLineageHeatmap(): plotLineageHeatmap

plotLineageNeighbors(): Lineage Plot for top neighbors

plotLineageQuery(): Lineage Plot: Heatmap of Queries vs Lineages

plotLineageSunburst(): Lineage Sunburst

plotStackedLineage(): Stacked Lineage Plot

plotSunburst() plotTreemap(): Create an interactive plotly from count data

plotUpSet(): UpSet Plot

prepareColumnParams(): prepareColumnParams

prepareSingleColumnParams(): prepareSingleColumnParams

proteinAcc2TaxID(): proteinAcc2TaxID

proteinAcc2TaxID_old(): proteinAcc2TaxID_old

readIPRScanTSV(): Read an interproscan output TSV with standardized column names and types

removeAsterisks(): Remove Asterisk

removeEmptyRows(): Remove Empty

removeTails(): Remove Tails

renameFA(): Rename the labels of fasta files

rename_fasta(): Rename the labels of fasta files

replaceQuestionMarks(): Replace QMs

reverseOperonSeq(): reverseOperon: Reverse the Direction of Operons in Genomic ContextSeq

runDeltaBlast(): Run DELTABLAST to find homologs for proteins of interest

runIPRScan(): runIPRScan

runRPSBlast(): Run RPSBLAST to generate domain architectures for proteins of interest

selectLongestDuplicate(): Pick Longer Duplicate

sendJobStatusEmail(): Sends a "job accepted" email to a user when their job is accepted, including details about the job submission and how to check its status.

shortenLineage(): shortenLineage

sinkReset(): Sink Reset

straightenOperonSeq(): straightenOperonSeq: Reverse Equalities in Genomic Context

themeGenes2(): themeGenes2

validateCountDF(): validateCountDF

wordcloud3(): plotWordCloud3

words2WordCounts(): words2WordCounts

writeMSA_AA2FA(): writeMSA_AA2FA

writeProcessRuntime2TSV(): writeProcessRuntime2TSV

writeProcessRuntime2YML(): writeProcessRuntime2YML