shiftFootprints {ORFik} | R Documentation

## Shift footprints by selected offsets

### Description

Function shifts footprints (GRanges) using specified offsets for every of the specified lengths. Reads that do not conform to the specified lengths are filtered out and rejected. Reads are resized to single base in 5' end fashion, treated as p site. This function takes account for junctions in cigars of the reads. Length of the footprint is saved in size' parameter of GRanges output. Footprints are also sorted according to their genomic position, ready to be saved as a ofst, bed or wig file.

### Usage

    shiftFootprints(footprints, shifts, sort = TRUE)

### Arguments

`footprints` | `GAlignments` object of RiboSeq reads
`shifts` | a data.frame / data.table with minimum 2 columns, fraction (selected_lengths) and selected_shifts (relative position). Output from `detectRibosomeShifts`
`sort` | logical, default TRUE. If False will keep original order of reads, and not sort output reads in increasing genomic location per chromosome and strand.

### Details

The two columns in the shift data.frame/data.table argument are:
- fraction Numeric vector of lengths of footprints you select for shifting.
- offsets_start Numeric vector of shifts for corresponding selected_lengths. eg. c(-10, -10) with selected_lengths of c(31, 32) means length of 31 will be shifted left by 10. Footprints of length 32 will be shifted right by 10.

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 `GRanges` object of shifted footprints, sorted and resized to 1bp of p-site, with metacolumn "size" indicating footprint size before shifting and resizing, sorted in increasing order.

### References

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4912-6

### See Also

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

### Examples

    # Basic run
    #shiftFootprints(footprints, shifts)
    # Full example
    ## Not run:
    # input path to gtf, or load it as TxDb.
    gtf_file <- system.file("extdata", "annotations.gtf", package = "ORFik")
    # load reads
    riboSeq_file <- system.file("extdata", "ribo-seq.bam", package = "ORFik")
    footprints <- GenomicAlignments::readGAlignments(
      riboSeq_file, param = ScanBamParam(flag = scanBamFlag(
        isDuplicate = FALSE, isSecondaryAlignment = FALSE)))
    # detect the shifts automagically
    shifts <- detectRibosomeShifts(footprints, gtf_file)
    # shift the RiboSeq footprints
    shiftedReads <- shiftFootprints(footprints, shifts)

    ## End(Not run)

[Package ORFik version 1.8.6 Index]