uORFSearchSpace {ORFik} | R Documentation

## Create search space to look for uORFs

### Description

Given a GRangesList of 5' UTRs or transcripts, reassign the start sites using max peaks from CageSeq data. A max peak is defined as new TSS if it is within boundary of 5' leader range, specified by 'extension' in bp. A max peak must also be higher than minimum CageSeq peak cutoff specified in 'filterValue'. The new TSS will then be the positioned where the cage read (with highest read count in the interval). If you want to include uORFs going into the CDS, add this argument too.

### Usage

    uORFSearchSpace(fiveUTRs, cage, extension = 1000, filterValue = 1,
      cds = NULL)

### Arguments

`fiveUTRs` | (GRangesList) The 5' leaders or transcript sequences
`cage` | Either a filePath for CageSeq file, or already loaded CageSeq peak data as GRanges.
`extension` | The maximum number of basses upstream of the TSS to search for CageSeq peak.
`filterValue` | The minimum number of reads on cage position, for it to be counted as possible new tss. (represented in score column in CageSeq data) If you already filtered, set it to 0.
`cds` | (GRangesList) CDS of relative fiveUTRs, applicable only if you want to extend 5' leaders downstream of CDS's, to allow upstream ORFs that can overlap into CDS's.

### Value

a GRangesList of newly assigned TSS for fiveUTRs, using CageSeq data.

### Examples

    # example 5' leader, notice exon_rank column
    fiveUTRs <- GenomicRanges::GRangesList(
      GenomicRanges::GRanges(seqnames = "chr1",
                             ranges = IRanges::IRanges(1000, 2000),
                             strand = "+",
                             exon_rank = 1))
    names(fiveUTRs) <- "tx1"

    # make fake CageSeq data from promoter of 5' leaders, notice score column
    cage <- GenomicRanges::GRanges(
      seqnames = "chr1",
      ranges =  IRanges::IRanges(500, 510),
      strand = "+",
      score = 10)

    # finally reassign TSS for fiveUTRs
    uORFSearchSpace(fiveUTRs, cage)

[Package ORFik version 1.4.1 Index]