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. |
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. |
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 |
bedToGR | Converts different type of files to Granges |
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 |
coverageByWindow | Compute coverage for every GRangesList subset. |
coveragePerTiling | Get coverage per group |
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) |
entropy | Calucalte entropy value of overlapping input reads. |
extendLeaders | Extend the leaders transcription start sites. |
extendsTSSexons | Extend first exon of each transcript with length specified |
filterCage | Filter peak of cage-data by value |
findCageUTRFivelen | Get length of leaders ordered after oldTxNames |
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. |
getStartStopWindows | Get Start and Stop codon within specified windows over CDS. |
groupGRangesBy | Group GRanges |
gSort | Sort a GRangesList, helper. |
hasHits | Hits from reads |
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 |
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 |
kozakSequenceScore | Make a score for each ORFs start region by proximity to Kozak |
lastExonEndPerGroup | Get last end per granges group |
lastExonPerGroup | Get last exon per GRangesList group |
lastExonStartPerGroup | Get last start per granges group |
longestORFs | Get longest ORF per stop site |
makeExonRanks | Make a meta column with exon ranks |
makeORFNames | Make ORF names per orf |
mapToGRanges | Map orfs to genomic coordinates |
matchNaming | Match naming of GRangesList |
metaWindow | Calculate metaplot coverage of reads around input GRangesList object. |
numExonsPerGroup | Get list of the number of exons per group |
orfID | Get id's for 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 |
parseCigar | Shift ribo-seq reads using cigar string |
pmapFromTranscriptF | Faster more secure version of mapFromTranscripts |
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 |
regroupRleList | Regroup rle from GRangesList |
remakeTxdbExonIds | Get new exon ids |
removeMetaCols | Removes meta columns |
removeTxdbExons | Remove exons in txList that are not in fiveUTRs |
restrictTSSByUpstreamLeader | Restrict extension of 5' UTRs to closest upstream leader end |
ribosomeReleaseScore | Ribosome Release Score (RRS) |
ribosomeStallingScore | Ribosome Stalling Score (RSS) |
riboTISCoverageProportion | Find proportion of reads per position in ORF TIS window |
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 |
startRegionString | Get -20,20 start region as DNA characters per gr 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. |
subset_to_frame | Subset GRanges to get desired frame. GRanges object should be beforehand tiled to size of 1. This subsetting takes account for strand. |
tile1 | Tile a GRangesList by 1 |
translationalEff | Translational efficiency |
txLen | Get transcript lengths |
txNames | Get transcript names from orf names |
txNamesWithLeaders | Get the transcripts that have minimum lengths of leaders and cds. |
txSeqsFromFa | Get transcript sequence from a GrangesList and a faFile or BSgenome |
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) |
validGRL | Helper Function to check valid GRangesList input |
widthPerGroup | Get list of widths per granges group |
windowPerGroup | Get window region of tx around point of gr |