# Open Reading Frames in Genomics

## Documentation for package ‘ORFik’ version 1.22.2

- 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 W

ORFik-package | ORFik for analysis of open reading frames.

## -- A --

artificial.orfs | Create small artificial orfs from cds
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'
browseSRA | Open SRA in browser for specific bioproject

## -- C --

codon_usage | Codon usage
codon_usage_exp | Codon analysis for ORFik experiment
codon_usage_plot | Plot codon_usage
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
collapseDuplicatedReads-method | Collapse duplicated reads
combn.pairs | Create all unique combinations pairs possible
computeFeatures | Get all main features in ORFik
computeFeaturesCage | Get all main features in ORFik
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
convert_bam_to_ofst | Convert libraries to ofst
convert_to_bigWig | Convert to BigWig
convert_to_covRle | Convert libraries to covRle
convert_to_covRleList | Convert libraries to covRleList objects
convert_to_fstWig | Convert to fstwig
correlation.plots | Correlation plots between all samples
cor_plot | Get correlation between columns
cor_table | Get correlation between columns
countOverlapsW | CountOverlaps with weights
countTable | Extract count table directly from experiment
countTable_regions | Make a list of count matrices from experiment
coverageByTranscriptC | coverageByTranscript with coverage input
coverageByTranscriptW | coverageByTranscript with weights
coverageHeatMap | Create a heatmap of coverage
coveragePerTiling | Get coverage per group
coverageScorings | Add a coverage scoring scheme
coverage_to_dt | Convert coverage RleList to data.table
covRle | Coverage Rlelist for both strands
covRle-class | Coverage Rle for both strands or single
covRleFromGR | Convert GRanges to covRle
covRleList | Coverage Rlelist for both strands
covRleList-class | List of covRle
create.experiment | Create an ORFik 'experiment'

## -- D --

defineTrailer | Defines trailers for ORF.
DEG.analysis | Run differential TE analysis
DEG.plot.static | Plot DEG result
DEG_model | Get DESeq2 model without running results
DEG_model_results | Get DESeq2 model results from DESeqDataSet
DEG_model_simple | Simple Fpkm ratio test DEG
design-method | Get experimental design Find the column/columns that create a separation between samples, by default skips replicate and choose first that is from either: libtype, condition, stage and fraction.
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.SRA | Download read libraries from SRA
download.SRA.metadata | Downloads metadata from SRA
DTEG.analysis | Run differential TE analysis
DTEG.plot | Plot DTEG result

## -- E --

entropy | Percentage of maximum entropy
envExp | Get ORFik experiment environment
envExp-method | Get ORFik experiment environment
envExp<- | Set ORFik experiment environment
envExp<--method | Set ORFik experiment environment
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.bigWig | Export as bigWig format
export.fstwig | Export as fstwig (fastwig) format
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.
extendTrailers | Extend the Trailers transcription stop sites
extract_run_id | Extract SRR/ERR/DRR run IDs from string

## -- F --

f | strandMode covRle
f-method | strandMode covRle
filepath | Get filepaths to ORFik experiment
filterExtremePeakGenes | Filter out transcript by a median filter
filterTranscripts | Filter transcripts by lengths
fimport | Load any type of sequencing reads
findFa | Convenience wrapper for Rsamtools FaFile
findMapORFs | Find ORFs and immediately map them to their genomic positions.
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
findUORFs_exp | 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
fix_malformed_gff | Fix a malformed gff file
flankPerGroup | Get flanks per group
floss | Fragment Length Organization Similarity Score
fpkm | Create normalizations of overlapping read counts.
fractionLength | Fraction Length
fread.bed | Load bed file as GRanges

## -- G --

gcContent | Get GC content
geneToSymbol | Get gene symbols from Ensembl gene ids
getGenomeAndAnnotation | Download genome (fasta), annotation (GTF) and contaminants
get_bioproject_candidates | Query eutils for bioproject IDs
get_silva_rRNA | Download Silva SSU & LSU sequences
groupGRangesBy | Group GRanges
groupings | Get number of ranges per group as an iteration

## -- H --

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.fstwig | Import region from fastwig
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
isInFrame | Find frame for each orf relative to cds
isOverlapping | Find frame for each orf relative to cds

## -- 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
length-method | length covRle
length-method | length covRleList
lengths-method | lengths covRle
lengths-method | lengths covRleList
libFolder | Get ORFik experiment library folder
libFolder-method | Get ORFik experiment library folder
libraryTypes | Which type of library type in 'experiment'?
list.experiments | List current experiment available
list.genomes | List genomes created with ORFik
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 --

makeORFNames | Make ORF names per orf
makeSummarizedExperimentFromBam | Make a count matrix from a library or experiment
makeTxdbFromGenome | Make txdb from genome
mergeFastq | Merge groups of Fastq /Fasta files
mergeLibs | Merge and save libraries of experiment
metadata.autnaming | Guess SRA metadata columns
metaWindow | Calculate meta-coverage of reads around input GRanges/List object.
model.matrix-method | Get experiment design model matrix

## -- N --

name | Get name of ORFik experiment
name-method | Get name of ORFik experiment
nrow-method | Internal nrow function for ORFik experiment Number of runs in experiment
numExonsPerGroup | Get list of the number of exons per group

## -- O --

ofst_merge | Merge multiple ofst file
optimizedTranscriptLengths | Load length and names of all transcripts
orfFrameDistributions | Find shifted Ribo-seq frame distributions
ORFik | ORFik for analysis of open reading frames.
ORFik.template.experiment | An ORFik experiment to see how it looks
ORFik.template.experiment.zf | 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-method | Get ORFik experiment organism
outputLibs | Output NGS libraries to R as variables

## -- P --

pcaExperiment | Simple PCA analysis
pmapFromTranscriptF | Faster pmapFromTranscript
pmapToTranscriptF | Faster pmapToTranscript
pSitePlot | Plot area around TIS as histogram

## -- Q --

QCfolder | Get ORFik experiment QC folder path
QCfolder-method | Get ORFik experiment QC folder path
QCreport | A post Alignment quality control of reads
QCstats | Load ORFik QC Statistics report
QCstats.plot | Make plot of ORFik QCreport

## -- R --

r | strandMode covRle
r-method | strandMode covRle
rankOrder | ORF rank in transcripts
read.experiment | Read ORFik 'experiment'
readBam | Custom bam reader
readBigWig | Custom bigWig 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
regionPerReadLength | Find proportion of reads per position per read length in region
remove.experiments | Remove ORFik experiment libraries load in R
resFolder | Get ORFik experiment main output directory
resFolder-method | Get ORFik experiment main output directory
RiboQC.plot | Quality control for pshifted Ribo-seq data
ribosomeReleaseScore | Ribosome Release Score (RRS)
ribosomeStallingScore | Ribosome Stalling Score (RSS)
ribo_fft | Get periodogram data per read length
ribo_fft_plot | Get periodogram plot per read length
rnaNormalize | Normalize a data.table of coverage by RNA seq per position
runIDs | Get SRR/DRR/ERR run ids from ORFik experiment
runIDs-method | Get SRR/DRR/ERR run ids from ORFik experiment

## -- S --

save.experiment | Save 'experiment' to disc
scaledWindowPositions | Scale (bin) windows to a meta window of given size
scoreSummarizedExperiment | Helper function for makeSummarizedExperimentFromBam
seqinfo-method | Seqinfo covRle Extracted from forward RleList
seqinfo-method | Seqinfo covRle Extracted from forward RleList
seqinfo-method | Seqinfo ORFik experiment Extracted from fasta genome index
seqlevels-method | Seqlevels covRle Extracted from forward RleList
seqlevels-method | Seqlevels covRleList Extracted from forward RleList
seqlevels-method | Seqlevels ORFik experiment Extracted from fasta genome index
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 | covRle show definition
show-method | covRleList show definition
show-method | experiment show definition
simpleLibs | Converted format of NGS libraries
sortPerGroup | Sort a GRangesList
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
strandMode-method | strandMode covRle
strandMode-method | strandMode covRle
strandPerGroup | Get list of strands per granges group
subsetToFrame | Subset GRanges to get desired frame.
symbols | Get ORFik experiment QC folder path
symbols-method | Get ORFik experiment QC folder path

## -- 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.
TOP.Motif.ecdf | TOP Motif ecdf plot
topMotif | TOP Motif detection
transcriptWindow | Make 100 bases size meta window for all libraries in experiment
translationalEff | Translational efficiency
trimming.table | Create trimming table
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

## -- 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