Open Reading Frames in Genomics


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Documentation for package ‘ORFik’ version 1.6.9

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

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 --

bamVarName Get library variable names from ORFik 'experiment'
bamVarNamePicker Get variable name per filepath in experiment
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 read 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
countTable Extract count table directly from experiment
coverageByTranscriptW Remake of coverageByTranscript
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
create.experiment Create a template for new ORFik 'experiment'

-- 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.
experiment experiment class definition
experiment-class experiment class definition
export.bedo Store GRanges object as .bedo
extendLeaders Extend the leaders transcription start sites.
extendsTSSexons Extend first exon of each transcript with length specified
extendTrailers Extend the Trailers transcription stop sites

-- F --

filterCage Filter peak of cage-data by value
filterTranscripts Filter transcripts by lengths
filterUORFs Remove uORFs that are false CDS hits
fimport Load any type of sequencing reads
findFa Convenience wrapper for Rsamtools FaFile
findFromPath Find all candidate library types filenames
findLibrariesInFolder Get all library files in folder
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.
findUORFs Find upstream ORFs from transcript annotation
findWigPairs Find pair of forward and reverse strand wig 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 read counts
fractionLength Fraction Length
fread.bed Load bed file as GRanges.

-- G --

gcContent Get GC content
getNGenesCoverage Get number of genes per coverage table
groupGRangesBy Group GRanges
groupings Get number of ranges per group as an iterator
gSort Sort a GRangesList, helper.

-- H --

hasHits Hits from reads

-- I --

import.bedo Load GRanges object from .bedo
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 --

kozakHeatmap Make sequence region heatmap relative to scoring
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
libraryTypes Which type of library type in 'experiment'?
loadRegion Load transcript region
loadRegions Get all regions of transcripts specified to environment
loadTranscriptType Load transcripts of given biotype
loadTxdb General loader for txdb
longestORFs Get longest ORF per stop site

-- M --

makeExonRanks Make grouping by exons ranks
makeORFNames Make ORF names per orf
makeSummarizedExperimentFromBam Make a count matrix from a library or experiment
mapToGRanges Map orfs to genomic coordinates
matchColors Match coloring of coverage plot
matchNaming Match naming of GRangesList
matchSeqStyle A wrapper for seqlevelsStyle
metaWindow Calculate meta-coverage of reads around input GRanges/List object.

-- N --

nrow-method Internal nrow function for ORFik experiment Number of runs in experiment
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.
ORFikQC A post Alignment quality control of reads
orfScore Get ORFscore for a GRangesList of ORFs
outputLibs Output bam/bed/bedo/wig files to R as variables
overlapsToCoverage Get overlaps and convert to Rle coverage list

-- P --

parseCigar Shift ribo-seq reads using cigar string
pasteDir A paste function for directories Makes sure slashes are corrected, and not doubled.
plotHelper Helper function for coverage plots
pmapFromTranscriptF Faster pmapFromTranscript
prettyScoring Prettify scoring name
pSitePlot Plot area around TIS as histogram

-- Q --

QCplots Correlation and coverage plots for ORFikQC

-- R --

rankOrder ORF rank in transcripts
read.experiment Read ORFik 'experiment'
readBam Custom bam reader
readWidths Get read widths
readWig Custom wig reader
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 after update of txdb
remove.experiments Remove bam/bed/wig files load in R as variables
remove.file_ext Remove file extension of path
removeMetaCols Removes meta columns
removeORFsWithinCDS Remove ORFs that are within cds
removeORFsWithSameStartAsCDS Remove ORFs that have same start site as the CDS
removeORFsWithSameStopAsCDS Remove ORFs that have same stop site as the CDS
removeORFsWithStartInsideCDS Remove ORFs that have start site within the CDS
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)
rnaNormalize Normalize a data.table of coverage by RNA seq per position

-- S --

save.experiment Save 'experiment' to disc
savePlot Helper function for writing plots to disc
scaledWindowPositions Scale (bin) windows to a meta window of given size
scoreSummarizedExperiment Helper function for makeSummarizedExperimentFromBam
seqnamesPerGroup Get list of seqnames per granges group
shiftFootprints Shift footprints by selected offsets
shiftFootprintsByExperiment Shift footprints of each file in experiment
show-method experiment show definition
simpleLibs Will make a simplified version of NGS libraries
sortPerGroup Sort a GRangesList
splitIn3Tx Create binned coverage of transcripts, split into the 3 parts.
startCodons Get the Start codons(3 bases) from a GRangesList of orfs grouped by orfs
startDefinition Returns start codon 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 codon 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.

-- T --

tile1 Tile each GRangesList group to 1-base resolution.
transcriptWindow Make 100 bases size meta window for all libraries in experiment
transcriptWindowPer Helper function for transcriptWindow
translationalEff Translational efficiency
txNames Get transcript names from orf names
txNamesToGeneNames Convert transcript names to gene 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 inside txdb object
updateTxdbStartSites Update start sites of leaders
upstreamFromPerGroup Get rest of objects upstream (inclusive)
upstreamOfPerGroup Get rest of objects upstream (exclusive)

-- V --

validateExperiments Validate ORFik 'experiment'
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 meta coverage plot of reads
windowPerGroup Get window region of GRanges object
windowPerReadLength Find proportion of reads per position per read length in window
windowPerTranscript Get a binned coverage window per transcript

-- X --

xAxisScaler Scale x axis correctly

-- Y --

yAxisScaler Scale y axis correctly