# Open Reading Frames in Genomics

## Documentation for package ‘ORFik’ version 1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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