toy_data {SplicingGraphs} | R Documentation

## Little helpers for quick access to the toy data included in the SplicingGraphs package

### Description

TODO

### Usage

    toy_genes_gff()
    toy_reads_sam()
    toy_reads_bam()
    toy_overlaps()

### Author(s)

H. Pagès

### See Also

This man page is part of the SplicingGraphs package. Please see `?`SplicingGraphs-package`` for an overview of the package and for an index of its man pages.

Other topics related to this man page and documented in other packages:

- The GRangesList class defined in the GenomicRanges package.

- The GAlignments and GAlignmentPairs classes defined in the GenomicAlignments package.

- The `makeTxDbFromGFF` function and the TxDb class defined in the GenomicFeatures package.

### Examples

    ## ---------------------------------------------------------------------
    ## A. LOAD THE TOY GENE MODEL AS A TxDb OBJECT AND PLOT IT
    ## ---------------------------------------------------------------------
    toy_genes_gff()

    ## Note that you can display the content of the file with:
    cat(readLines(toy_genes_gff()), sep="\n")

    library(GenomicFeatures)
    suppressWarnings(
      txdb <- makeTxDbFromGFF(toy_genes_gff())
    )

    ## Plot all the transcripts in the gene model:
    plotTranscripts(txdb)

    ## ---------------------------------------------------------------------
    ## B. LOAD THE TOY READS AS A GAlignments OBJECT AND PLOT THEM
    ## ---------------------------------------------------------------------
    ## The reads are single-end reads. They are assumed to come from an
    ## RNA-seq experiment and to have been aligned to the exact same
    ## reference genome that the above toy gene model is based on.
    toy_reads_sam()
    toy_reads_bam()
    gal <- readGAlignments(toy_reads_bam(), use.names=TRUE)

    plotTranscripts(txdb, reads=gal)
    plotTranscripts(txdb, reads=gal, from=1, to=320)

    ## ---------------------------------------------------------------------
    ## C. FIND THE OVERLAPS BETWEEN THE TOY READS AND THE TOY GENE MODEL
    ## ---------------------------------------------------------------------
    grl <- grglist(gal, order.as.in.query=TRUE)
    ex_by_tx <- exonsBy(txdb, by="tx", use.names=TRUE)

    ## Most of the times the RNA-seq protocol is unstranded so the strand
    ## reported in the BAM file for each alignment is meaningless. Thus we
    ## should call findOverlaps() with 'ignore.strand=TRUE':
    ov0 <- findOverlaps(grl, ex_by_tx, ignore.strand=TRUE)

    ## Sort and put the overlaps in a data.frame to make them easier to
    ## read:
    ov0 <- sort(ov0)
    df0 <- data.frame(QNAME=names(grl)[queryHits(ov0)],
                      tx_id=names(ex_by_tx)[subjectHits(ov0)],
                      stringsAsFactors=FALSE)
    head(df0)

    ## These overlaps have been manually checked and included in the
    ## SplicingGraphs package. They can be loaded with the toy_overlaps()
    ## helper:
    toy_ov <- toy_overlaps()
    head(toy_ov)
    stopifnot(identical(df0, toy_ov[ , 1:2]))

    ## ---------------------------------------------------------------------
    ## D. DETECT THE OVERLAPS THAT ARE COMPATIBLE WITH THE GENE MODEL
    ## ---------------------------------------------------------------------
    ## First we encode the overlaps:
    ovenc0 <- encodeOverlaps(grl, ex_by_tx, hits=ov0,
                             flip.query.if.wrong.strand=TRUE)
    ovenc0

    ## Each encoding tells us whether the corresponding overlap is
    ## compatible or not with the gene model:
    ov0_is_comp <- isCompatibleWithSplicing(ovenc0)
    head(ov0_is_comp)

    ## Overlap compatibility has also been manually checked and included in
    ## the table returned by toy_overlaps():
    stopifnot(identical(ov0_is_comp, toy_ov[ , 3]))

[Package SplicingGraphs version 1.20.0 Index]