Open Reading Frames in Genomics


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Documentation for package ‘ORFik’ version 1.4.1

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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.
allFeaturesHelper Calculate the features in computeFeatures
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
coverageGroupings Get grouping for a coverage table in ORFik
coverageHeatMap Create a heatmap of coverage
coveragePerTiling Get coverage per group
coverageScorings Add a coverage scoring scheme

-- 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 per GRanges.
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
filterTranscripts Get the transcripts with accepted lengths of leaders, cds and trailer.
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 --

gcContent Get GC content
groupGRangesBy Group GRanges
groupings Get number of ranges per group as an iterator
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
is.ORF Check if all requirements for an ORFik ORF is accepted.
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
loadRegion Load transcript region
loadTxdb General loader for txdb
longestORFs Get longest ORF per stop site

-- M --

makeExonRanks Make grouping for exon structures.
makeORFNames Make ORF names per orf
mapToGRanges Map orfs to genomic coordinates
matchNaming Match naming of GRangesList
metaWindow Calculate meta-coverage of reads around input GRanges/List object.

-- N --

numCodons Get number of codons
numExonsPerGroup Get list of the number of exons per group

-- O --

optimizeReads Find optimized subset of valid reads
orfID Get id's for each 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 pmapFromTranscript
pSitePlot Plot area around TIS for p-shifted reads

-- 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
remakeTxdbExonIds Get new exon ids
removeMetaCols Removes meta columns
removeTxdbExons Remove exons in txList that are not in fiveUTRs
removeTxdbTranscripts Remove specific transcripts in txdb List
restrictTSSByUpstreamLeader Restrict extension of 5' UTRs to closest upstream leader end
ribosomeReleaseScore Ribosome Release Score (RRS)
ribosomeStallingScore Ribosome Stalling Score (RSS)

-- S --

savePlot Helper function for writing plots to disc
scaledWindowPositions Scale windows to a meta window of size
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
startRegion Start region as GRangesList
startRegionCoverage Start region coverage
startRegionString Get start region as DNA-strings per GRanges 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.
subsetToFrame 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 each GRangesList group to 1-base resolution.
translationalEff Translational efficiency
txNames Get transcript names from orf names
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
validSeqlevels Helper function to find overlaping seqlevels

-- W --

widthPerGroup Get list of widths per granges group
windowCoveragePlot Get coverage window plot of reads
windowPerGroup Get window region of GRanges object
windowPerReadLength Find proportion of reads per position in window
windowPerTranscript Get coverage window per transcript