shiftFootprints: Shift footprints by selected offsets

In JokingHero/ORFik: Open Reading Frames in Genomics

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 and soft clips 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, covRle, bed or wig file.

Usage

shiftFootprints(footprints, shifts, sort = TRUE)

Arguments

footprints	GAlignments object of RiboSeq reads - footprints, can also be path to the .bam /.ofst file. If GAlignment object has a meta column called "score", this will be used as replicate numbering for that read. So be careful if you have custom files with score columns, with another meaning.
shifts	a data.frame / data.table with minimum 2 columns, fraction (selected read lengths) and offsets_start (relative position in nt). Output from detectRibosomeShifts. Run ORFik::shifts_load(df)[[1]] for an example of input.
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(), shiftPlots(), shifts_load(), shifts_save()

Examples

## Basic run
# Transcriptome annotation ->
gtf_file <- system.file("extdata/references/danio_rerio", "annotations.gtf", package = "ORFik")
# Ribo seq data ->
riboSeq_file <- system.file("extdata/Danio_rerio_sample", "ribo-seq.bam", package = "ORFik")
## Not run: 
footprints <- readBam(riboSeq_file)

# detect the shifts automagically
shifts <- detectRibosomeShifts(footprints, gtf_file)
# shift the RiboSeq footprints
shiftedReads <- shiftFootprints(footprints, shifts)

## End(Not run)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.