detectRibosomeShifts {ORFik} | R Documentation

## Detect ribosome shifts

### Description

Utilizes periodicity measurement (fourier transform) and change point analysis to detect ribosomal footprint shifts for each of the ribosomal read lengths. Returns subset of read lengths and their shifts for which top covered transcripts follow periodicity measure. Each shift value assumes 5' anchoring of the reads, so that output offsets values will shift 5' anchored footprints to be on the p-site of the ribosome.

### Usage

    detectRibosomeShifts(
      footprints,
      txdb,
      start = TRUE,
      stop = FALSE,
      top_tx = 10L,
      minFiveUTR = 30L,
      minCDS = 150L,
      minThreeUTR = 30L,
      firstN = 150L,
      tx = NULL
    )

### Arguments

`footprints` | (GAlignments) object of RiboSeq reads - footprints, can also be path to the file.
`txdb` | a TxDb file, a path to one of: (.gtf ,.gff, .gff2, .gff2, .db or .sqlite) or an ORFik experiment
`start` | (logical) Whether to include predictions based on the start codons. Default TRUE.
`stop` | (logical) Whether to include predictions based on the stop codons. Default FASLE. Only use if there exists 3' UTRs for the annotation.
`top_tx` | (integer) Specify which transcripts to use for estimation of the shifts. By default we take top 10 top covered transcripts as they represent less noisy dataset. This is only applicable when there are more than 1000 transcripts.
`minFiveUTR` | (integer) minimum bp for 5' UTR during filtering for the transcripts. Set to NULL if no 5' UTRs exists for annotation.
`minCDS` | (integer) minimum bp for CDS during filtering for the transcripts
`minThreeUTR` | (integer) minimum bp for 3' UTR during filtering for the transcripts. Set to NULL if no 3' UTRs exists for annotation.
`firstN` | (integer) Represents how many bases of the transcripts downstream of start codons to use for initial estimation of the periodicity.
`tx` | a GRangesList, if you do not have 5' UTRs in annotation, send your own version. Example: extendLeaders(tx, 30) Where 30 bases will be new "leaders". Since each original transcript was either only CDS or non-coding (filtered out).

### Details

Check out vignette for the examples of plotting RiboSeq metaplots over start and stop codons, so that you can verify visually whether this function detects correct shifts.

NOTE: It will remove softclips from valid width, the CIGAR 3S30M is qwidth 33, but will remove 3S so final read width is 30 in ORFik.

### Value

a data.table with lengths of footprints and their predicted coresponding offsets

### See Also

Other pshifting: `changePointAnalysis()`, `shiftFootprintsByExperiment()`, `shiftFootprints()`

### Examples

    ## Not run:
    # Transcriptome annotation ->
    gtf_file <- system.file("extdata", "annotations.gtf", package = "ORFik")
    # The ribo seq file, usually .bam file ->
    riboSeq_file <- system.file("extdata", "ribo-seq.bam", package = "ORFik")
    footprints <- GenomicAlignments::readGAlignments(
      riboSeq_file, param = ScanBamParam(flag = scanBamFlag(
        isDuplicate = FALSE, isSecondaryAlignment = FALSE)))

    detectRibosomeShifts(footprints, gtf_file, stop = TRUE)

    # Without 5' Annotation
    library(GenomicFeatures)

    txdb <- loadTxdb(gtf_file)
    tx <- exonsBy(txdb, by = "tx", use.names = TRUE)
    tx <- extendLeaders(tx, 30)
    # Now run function, without 5' and 3' UTRs
    detectRibosomeShifts(footprints, txdb, start = TRUE, minFiveUTR = NULL,
                         minCDS = 150L, minThreeUTR = NULL, firstN = 150L,
                         tx = tx)

    ## End(Not run)

[Package ORFik version 1.6.9 Index]