# Open Reading Frames in Genomics

## Documentation for package ‘ORFik’ version 1.10.13

- 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 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 function
artificial.orfs | Create small artificial orfs from cds
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 bed style data.frame to Granges

## -- C --

cellLineNames | Get cell-line name variants
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
collapse.by.scores | Merge reads by sum of existing scores
collapse.fastq | Very fast fastq/fasta collapser
collapseDuplicatedReads | Collapse duplicated reads
collapseDuplicatedReads-method | Collapse duplicated reads
collapseDuplicatedReads-method | Collapse duplicated reads
collapseDuplicatedReads-method | Collapse duplicated reads
combn.pairs | Create all unique combinations pairs possible
computeFeatures | Get all possible features in ORFik
computeFeaturesCage | Get all possible features in ORFik
conditionNames | Get condition name variants
config | Read directory config for ORFik experiments
config.exper | Set directories for experiment
config.save | Save/update directory config for ORFik experiments
convertLibs | Converted format of NGS libraries
convertToOneBasedRanges | Convert a GRanges Object to 1 width reads
correlation.plots | Correlation plots between all samples
countOverlapsW | CountOverlaps with weights
countTable | Extract count table directly from experiment
countTable_regions | Make a list of count matrices from experiment
coverageByTranscriptW | coverageByTranscript with weights
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 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
download.ebi | Faster download of fastq files
download.SRA | Download read libraries from SRA
download.SRA.metadata | Downloads metadata from SRA
downstreamFromPerGroup | Get rest of objects downstream (inclusive)
downstreamN | Restrict GRangesList
downstreamOfPerGroup | Get rest of objects downstream (exclusive)
DTEG.analysis | Run differential TE analysis
DTEG.plot | Plot DTEG result

## -- E --

entropy | Percentage of maximum entropy
exists.ftp.file.fast | A copy of biomartr ftp check
experiment | experiment class definition
experiment-class | experiment class definition
experiment.colors | Decide color for libraries by grouping
export.bed12 | Export as bed12 format
export.bedo | Store GRanges object as .bedo
export.bedoc | Store GAlignments object as .bedoc
export.ofst | Store GRanges / GAlignments object as .ofst
export.ofst-method | Store GRanges / GAlignments object as .ofst
export.ofst-method | Store GRanges / GAlignments object as .ofst
export.ofst-method | Store GRanges / GAlignments object as .ofst
export.wiggle | Export as wiggle format
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 --

filepath | Get filepaths to ORFik experiment
filterCage | Filter peak of cage-data by value
filterExtremePeakGenes | Filter out transcript by a median filter
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/folders of given types
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
findNGSPairs | Find pair of forward and reverse strand wig / bed files and paired end bam files split in two
findORFs | Find Open Reading Frames.
findORFsFasta | Finds Open Reading Frames in fasta files.
findPeaksPerGene | Find peaks per gene
findUORFs | Find upstream ORFs from transcript annotation
find_url_ebi | Locates and check if fastq files exists in ebi
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
footprints.analysis | Pre shifting plot analysis
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
getGAlignments | Internal GAlignments loader from fst data.frame
getGAlignmentsPairs | Internal GAlignmentPairs loader from fst data.frame
getGenomeAndAnnotation | Download genome (fasta), annotation (GTF) and contaminants
getGRanges | Internal GRanges loader from fst data.frame
getNGenesCoverage | Get number of genes per coverage table
getWeights | Get weights from a subject GenomicRanges object
get_genome_fasta | Download genome (fasta), annotation (GTF) and contaminants
get_genome_gtf | Download genome (fasta), annotation (GTF) and contaminants
get_noncoding_rna | Download genome (fasta), annotation (GTF) and contaminants
get_phix_genome | Download genome (fasta), annotation (GTF) and contaminants
get_silva_rRNA | Download Silva SSU & LSU sequences
groupGRangesBy | Group GRanges
groupings | Get number of ranges per group as an iteration
gSort | Sort a GRangesList, helper.

## -- H --

hasHits | Hits from reads
heatMapL | Coverage heatmap of multiple libraries
heatMapRegion | Create coverage heatmaps of specified region
heatMap_single | Coverage heatmap of single libraries

## -- I --

import.bedo | Load GRanges object from .bedo
import.bedoc | Load GAlignments object from .bedoc
import.ofst | Load GRanges / GAlignments object from .ofst
importGtfFromTxdb | Import the GTF / GFF that made the txdb
initiationScore | Get initiation score for a GRangesList of ORFs
insideOutsideORF | Inside/Outside score (IO)
install.fastp | Download and prepare fastp trimmer
install.sratoolkit | Download sra toolkit
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.
is.range | Helper function to check for ranged object
isInFrame | Find frame for each orf relative to cds
isOverlapping | Find frame for each orf relative to cds
isPeriodic | Find if there is a periodicity of 3 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
kozak_IR_ranking | Rank kozak initiation sequences

## -- L --

lastExonEndPerGroup | Get last end per granges group
lastExonPerGroup | Get last exon per GRangesList group
lastExonStartPerGroup | Get last start per granges group
libNames | Get library name variants
libraryTypes | Which type of library type in 'experiment'?
list.experiments | List current experiment available
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 --

mainNames | Get main name from variant name
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
mergeFastq | Merge groups of Fastq /Fasta files
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.
ORFik.template.experiment | An ORFik experiment to see how it looks
ORFikQC | A post Alignment quality control of reads
orfScore | Get ORFscore for a GRangesList of ORFs
organism.df | Get organism of the ORFik experiment
outputLibs | Output bam/bed/bedo/bedoc/ofst/wig files to R as variables

## -- P --

pasteDir | A paste function for directories Makes sure slashes are corrected, and not doubled.
percentage_to_ratio | Convert percentage to ratio of 1
plotHelper | Helper function for coverage plots
pmapFromTranscriptF | Faster pmapFromTranscript
pmapToTranscriptF | Faster pmapToTranscript
prettyScoring | Prettify scoring name
pseudo.transform | Transform object
pSitePlot | Plot area around TIS as histogram

## -- Q --

QCplots | Correlation and coverage plots for ORFikQC
QCreport | A post Alignment quality control of reads
QCstats | Load ORFik QC Statistics report
QCstats.plot | Make plot of ORFik QCreport
QC_count_tables | Create count table info for QC report

## -- R --

rankOrder | ORF rank in transcripts
read.experiment | Read ORFik 'experiment'
readBam | Custom bam reader
readLengthTable | Make table of readlengths
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
regionPerReadLength | Find proportion of reads per position per read length in region
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
rename.SRA.files | Rename SRA files from metadata
repNames | Get replicate name variants
restrictTSSByUpstreamLeader | Restrict extension of 5' UTRs to closest upstream leader end
reverseMinusStrandPerGroup | Reverse minus strand
RiboQC.plot | Quality control for pshifted Ribo-seq data
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
shiftPlots | Plot shifted heatmaps per library
shifts.load | Load the shifts from experiment
show-method | experiment show definition
simpleLibs | Converted format of NGS libraries
sortPerGroup | Sort a GRangesList
splitIn3Tx | Create binned coverage of transcripts, split into the 3 parts.
stageNames | Get stage name variants
STAR.align.folder | Align all libraries in folder with STAR
STAR.align.single | Align single or paired end pair with STAR
STAR.allsteps.multiQC | Create STAR multiQC plot and table
STAR.index | Create STAR genome index
STAR.install | Download and prepare STAR
STAR.multiQC | Create STAR multiQC plot and table
STAR.remove.crashed.genome | Remove crashed STAR genome
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
stopRegion | Stop region as GRangesList
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 --

te.plot | Translational efficiency plots
te.table | Create a TE table
te_rna.plot | Translational efficiency plots
tile1 | Tile each GRangesList group to 1-base resolution.
tissueNames | Get tissue name variants
TOP.Motif.ecdf | TOP Motif ecdf plot
topMotif | TOP Motif detection
transcriptWindow | Make 100 bases size meta window for all libraries in experiment
transcriptWindow1 | Meta coverage over all transcripts
transcriptWindowPer | Helper function for transcriptWindow
translationalEff | Translational efficiency
trimming.table | Create trimming table
trim_detection | Add trimming info to QC report
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