uORFSearchSpace: Create search space to look for uORFs

In JokingHero/ORFik: Open Reading Frames in Genomics

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 (if CAGE is given). 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 = NULL,
  extension = 1000,
  filterValue = 1,
  restrictUpstreamToTx = FALSE,
  removeUnused = FALSE,
  cds = NULL
)

Arguments

fiveUTRs	(GRangesList) The 5' leaders or full transcript sequences
cage	Either a filePath for the CageSeq file as .bed .bam or .wig, with possible compressions (".gzip", ".gz", ".bgz"), or already loaded CageSeq peak data as GRanges or GAlignment. NOTE: If it is a .bam file, it will add a score column by running: convertToOneBasedRanges(cage, method = "5prime", addScoreColumn = TRUE) The score column is then number of replicates of read, if score column is something else, like read length, set the score column to NULL first.
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.
restrictUpstreamToTx	a logical (FALSE). If TRUE: restrict leaders to not extend closer than 5 bases from closest upstream leader, set this to TRUE.
removeUnused	logical (FALSE), if False: (standard is to set them to original annotation), If TRUE: remove leaders that did not have any cage support.
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.

See Also

Other uorfs: addCdsOnLeaderEnds(), filterUORFs(), removeORFsWithSameStartAsCDS(), removeORFsWithSameStopAsCDS(), removeORFsWithStartInsideCDS(), removeORFsWithinCDS()

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)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.