scaleRanges: Scale spliced ranges to genome coordinates
In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description Usage Arguments Value Author(s) See Also Examples

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.

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

`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.

Object of class GRangesList

Thomas Girke

predORF

## 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)