Open Reading Frames in Genomics


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Documentation for package ‘ORFik’ version 1.2.1

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A B C D E F G H I K L M N O P R S T U V W

ORFik-package ORFik for analysis of open reading frames.

-- A --

addCdsOnLeaderEnds Extends leaders downstream
addNewTSSOnLeaders add cage max peaks as new transcript start sites for each 5' leader (*) strands are not supported, since direction must be known.
assignAnnotations Overlaps GRanges object with provided annotations.
assignFirstExonsStartSite Reassign the start positions of the first exons per group in grl
assignLastExonsStopSite Reassign the stop positions of the last exons per group
assignTSSByCage Input a txdb and add a 5' leader for each transcript, that does not have one.
asTX Map genomic to transcript coordinates by reference

-- B --

bedToGR Converts different type of files to Granges

-- C --

changePointAnalysis Get the offset for specific RiboSeq read width
checkRFP Helper Function to check valid RFP input
checkRNA Helper Function to check valid RNA input
codonSumsPerGroup Get hits per codon
computeFeatures Get all possible features in ORFik
computeFeaturesCage Get all possible features in ORFik
convertToOneBasedRanges Convert a GRanges Object to 1 width reads
coverageByWindow Compute coverage for every GRangesList subset.
coveragePerTiling Get coverage per group

-- D --

defineIsoform Overlaps GRanges object with provided annotations.
defineTrailer Defines trailers for ORF.
detectRibosomeShifts Detect ribosome shifts
disengagementScore Disengagement score (DS)
distToCds Get distances between ORF ends and starts of their transcripts cds'.
distToTSS Get distances between ORF Start and TSS of its transcript
downstreamFromPerGroup Get rest of objects downstream (inclusive)
downstreamN Restrict GRangesList
downstreamOfPerGroup Get rest of objects downstream (exclusive)

-- E --

entropy Calucalte entropy value of overlapping input reads.
extendLeaders Extend the leaders transcription start sites.
extendsTSSexons Extend first exon of each transcript with length specified

-- F --

filterCage Filter peak of cage-data by value
findCageUTRFivelen Get length of leaders ordered after oldTxNames
findFa Convenience wrapper for Rsamtools FaFile
findMapORFs Find ORFs and immediately map them to their genomic positions.
findMaxPeaks Find max peak for each transcript, returns as data.table, without names, but with index
findNewTSS Finds max peaks per trancsript from reads in the cagefile
findORFs Find Open Reading Frames.
findORFsFasta Finds Open Reading Frames in fasta files.
firstEndPerGroup Get first end per granges group
firstExonPerGroup Get first exon per GRangesList group
firstStartPerGroup Get first start per granges group
floss Fragment Length Organization Similarity Score
fpkm Create normalizations of overlapping read counts.
fpkm_calc Create normalizations of counts
fractionLength Fraction Length
fread.bed Load bed file as GRanges.

-- G --

getStartStopWindows Get Start and Stop codon within specified windows over CDS.
groupGRangesBy Group GRanges
gSort Sort a GRangesList, helper.

-- H --

hasHits Hits from reads

-- I --

initiationScore Get initiation score for a GRangesList of ORFs
insideOutsideORF Inside/Outside score (IO)
is.grl Helper function to check for GRangesList
is.gr_or_grl Helper function to check for GRangesList or GRanges class
isInFrame Find frame for each orf relative to cds
isOverlapping Find frame for each orf relative to cds
isPeriodic Find if there is periodicity in the vector

-- K --

kozakSequenceScore Make a score for each ORFs start region by proximity to Kozak

-- L --

lastExonEndPerGroup Get last end per granges group
lastExonPerGroup Get last exon per GRangesList group
lastExonStartPerGroup Get last start per granges group
longestORFs Get longest ORF per stop site

-- M --

makeExonRanks Make a meta column with exon ranks
makeORFNames Make ORF names per orf
mapToGRanges Map orfs to genomic coordinates
matchNaming Match naming of GRangesList
metaWindow Calculate metaplot coverage of reads around input GRangesList object.

-- N --

numExonsPerGroup Get list of the number of exons per group

-- O --

orfID Get id's for orf
ORFik ORFik for analysis of open reading frames.
orfScore Get ORFscore for a GRangesList of ORFs
overlapsToCoverage Get overlaps and convert to coverage list

-- P --

parseCigar Shift ribo-seq reads using cigar string
pmapFromTranscriptF Faster more secure version of mapFromTranscripts

-- R --

rankOrder ORF rank in transcripts
readWidths Get RiboSeq widths
reassignTSSbyCage Reassign all Transcript Start Sites (TSS)
reassignTxDbByCage Input a txdb and reassign the TSS for each transcript by CAGE
reduceKeepAttr Reduce GRanges / GRangesList
regroupRleList Regroup rle from GRangesList
remakeTxdbExonIds Get new exon ids
removeMetaCols Removes meta columns
removeTxdbExons Remove exons in txList that are not in fiveUTRs
restrictTSSByUpstreamLeader Restrict extension of 5' UTRs to closest upstream leader end
ribosomeReleaseScore Ribosome Release Score (RRS)
ribosomeStallingScore Ribosome Stalling Score (RSS)
riboTISCoverageProportion Find proportion of reads per position in ORF TIS window

-- S --

seqnamesPerGroup Get list of seqnames per granges group
shiftFootprints Shift footprints by selected offsets
sortPerGroup Sort a GRangesList
startCodons Get the Start codons(3 bases) from a GRangesList of orfs grouped by orfs
startDefinition Returns start definitions
startRegionString Get -20,20 start region as DNA characters per gr group
startSites Get the start sites from a GRangesList of orfs grouped by orfs
stopCodons Get the Stop codons (3 bases) from a GRangesList of orfs grouped by orfs
stopDefinition Returns stop definitions
stopSites Get the stop sites from a GRangesList of orfs grouped by orfs
strandBool Get logical list of strands
strandPerGroup Get list of strands per granges group
subsetCoverage Subset GRanges to get coverage.
subset_to_frame Subset GRanges to get desired frame. GRanges object should be beforehand tiled to size of 1. This subsetting takes account for strand.

-- T --

tile1 Tile a GRangesList by 1
translationalEff Translational efficiency
txLen Get transcript lengths
txNames Get transcript names from orf names
txNamesWithLeaders Get the transcripts that have minimum lengths of leaders and cds.
txSeqsFromFa Get transcript sequence from a GrangesList and a faFile or BSgenome

-- U --

uniqueGroups Get the unique set of groups in a GRangesList
uniqueOrder Get unique ordering for GRangesList groups
unlistGrl Safe unlist
uORFSearchSpace Create search space to look for uORFs
updateTxdbRanks Update exon ranks of exon data.frame
updateTxdbStartSites Update start sites of leaders
upstreamFromPerGroup Get rest of objects upstream (inclusive)
upstreamOfPerGroup Get rest of objects upstream (exclusive)

-- V --

validGRL Helper Function to check valid GRangesList input

-- W --

widthPerGroup Get list of widths per granges group
windowPerGroup Get window region of tx around point of gr