scaleRanges {systemPipeR} | R Documentation

## Scale spliced ranges to genome coordinates

### Description

Function to scale mappings of spliced features (query ranges) to their corresponding genome coordinates (subject ranges). The method accounts for introns in the subject ranges that are absent in the query ranges. A use case example are uORFs predicted in the 5' UTRs sequences using `predORF`. These query ranges are given relative to the 5' UTR sequence. The `scaleRanges` function will scale them to the corresponding genome coordinates. This way they can be used in RNA-Seq expression experiments like other gene ranges.

### Usage

    scaleRanges(subject, query, type = "custom", verbose = TRUE)

### Arguments

`subject` | Genomic ranges provided as `GRangesList` object. Their name and length requirements are described under `query`.
`query` | Feature level ranges provided as `GRangesList` object. The names of the query ranges need to match the names of the `GRangesList` object assigened to the `subject` argument. In addition, the length of each `query` range cannot exceed the total length of the corresponding `subject` range set.
`type` | Feature name to use in `type` column of `GRangesList` result.
`verbose` | The setting `verbose=FALSE` suppresses all print messages.

### Value

Object of class `GRangesList`

### Author(s)

Thomas Girke

### See Also

`predORF`

### Examples

    ## Usage for simple example
    subject <- GRanges(seqnames="Chr1", IRanges(c(5,15,30),c(10,25,40)), strand="+")
    query <- GRanges(seqnames="myseq", IRanges(1, 9), strand="+")
    scaleRanges(GRangesList(myid1=subject), GRangesList(myid1=query), type="test")

    ## Not run:
    ## Usage for more complex example
    library(GenomicFeatures); library(systemPipeRdata)
    gff <- system.file("extdata/annotation", "tair10.gff", package="systemPipeRdata")
    txdb <- makeTxDbFromGFF(file=gff, format="gff3", organism="Arabidopsis")
    futr <- fiveUTRsByTranscript(txdb, use.names=TRUE)
    genome <- system.file("extdata/annotation", "tair10.fasta", package="systemPipeRdata")
    dna <- extractTranscriptSeqs(FaFile(genome), futr)
    uorf <- predORF(dna, n="all", mode="orf", longest_disjoint=TRUE, strand="sense")
    grl_scaled <- scaleRanges(subject=futr, query=uorf, type="uORF", verbose=TRUE)
    export.gff3(unlist(grl_scaled), "uorf.gff")

    ## End(Not run)

[Package systemPipeR version 1.16.1 Index]