findCompatibleOverlaps-methods {GenomicAlignments} | R Documentation

## Finding hits between reads and transcripts that are compatible with the splicing of the transcript

### Description

In the context of an RNA-seq experiment, `findCompatibleOverlaps` (or `countCompatibleOverlaps`) can be used for finding (or counting) hits between reads and transcripts that are compatible with the splicing of the transcript.

### Usage

    findCompatibleOverlaps(query, subject)
    countCompatibleOverlaps(query, subject)

### Arguments

`query` | A GAlignments or GAlignmentPairs object representing the aligned reads.
`subject` | A GRangesList object representing the transcripts.

### Details

`findCompatibleOverlaps` is a specialized version of `findOverlaps` that uses `encodeOverlaps` internally to keep only the hits where the junctions in the aligned read are compatible with the splicing of the annotated transcript.

The topic of working with overlap encodings is covered in details in the "OverlapEncodings" vignette located this package (GenomicAlignments) and accessible with `vignette("OverlapEncodings")`.

### Value

A Hits object for `findCompatibleOverlaps`.

An integer vector parallel to (i.e. same length as) `query` for `countCompatibleOverlaps`.

### Author(s)

Hervé Pagès

### See Also

- The `findOverlaps` generic function defined in the IRanges package.

- The `encodeOverlaps` generic function and OverlapEncodings class.

- The "OverlapEncodings" vignette in this package.

- GAlignments and GAlignmentPairs objects.

- GRangesList objects in the GenomicRanges package.

### Examples

    ## Here we only show a simple example illustrating the use of
    ## countCompatibleOverlaps() on a very small data set. Please
    ## refer to the "OverlapEncodings" vignette in the GenomicAlignments
    ## package for a comprehensive presentation of "overlap
    ## encodings" and related tools/concepts (e.g. "compatible"
    ## overlaps, "almost compatible" overlaps etc...), and for more
    ## examples.

    ## sm_treated1.bam contains a small subset of treated1.bam, a BAM
    ## file containing single-end reads from the "Pasilla" experiment
    ## (RNA-seq, Fly, see the pasilla data package for the details)
    ## and aligned to reference genome BDGP Release 5 (aka dm3 genome on
    ## the UCSC Genome Browser):
    sm_treated1 <- system.file("extdata", "sm_treated1.bam",
                               package="GenomicAlignments", mustWork=TRUE)

    ## Load the alignments:
    flag0 <- scanBamFlag(isDuplicate=FALSE, isNotPassingQualityControls=FALSE)
    param0 <- ScanBamParam(flag=flag0)
    gal <- readGAlignments(sm_treated1, use.names=TRUE, param=param0)

    ## Load the transcripts (IMPORTANT: Like always, the reference genome
    ## of the transcripts must be *exactly* the same as the reference
    ## genome used to align the reads):
    library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
    txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
    exbytx <- exonsBy(txdb, by="tx", use.names=TRUE)

    ## Number of "compatible" transcripts per alignment in 'gal':
    gal_ncomptx <- countCompatibleOverlaps(gal, exbytx)
    mcols(gal)$ncomptx <- gal_ncomptx
    table(gal_ncomptx)
    mean(gal_ncomptx >= 1)
    ## --> 33% of the alignments in 'gal' are "compatible" with at least
    ## 1 transcript in 'exbytx'.

    ## Keep only alignments compatible with at least 1 transcript in
    ## 'exbytx':
    compgal <- gal[gal_ncomptx >= 1]
    head(compgal)

[Package GenomicAlignments version 1.22.1 Index]