reassignTxDbByCage: Input a txdb and reassign the TSS for each transcript by CAGE

In JokingHero/ORFik: Open Reading Frames in Genomics

Input a txdb and reassign the TSS for each transcript by CAGE

Description

Given a TxDb object, reassign the start site per transcript 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).

Usage

reassignTxDbByCage(
  txdb,
  cage,
  extension = 1000,
  filterValue = 1,
  restrictUpstreamToTx = FALSE,
  removeUnused = FALSE,
  preCleanup = TRUE
)

Arguments

txdb	a TxDb file, a path to one of: (.gtf ,.gff, .gff2, .gff2, .db or .sqlite) or an ORFik experiment
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.
preCleanup	logical (TRUE), if TRUE, remove all reads in region (-5:-1, 1:5) of all original tss in leaders. This is to keep original TSS if it is only +/- 5 bases from the original.

Details

Note: If you used CAGEr, you will get reads of a probability region, with always score of 1. Remember then to set filterValue to 0. And you should use the 5' end of the read as input, use: ORFik:::convertToOneBasedRanges(cage)

Value

a TxDb obect of reassigned transcripts

See Also

Other CAGE: assignTSSByCage(), reassignTSSbyCage()

Examples

 ## Not run: 
 library(GenomicFeatures)
 # Get the gtf txdb file
 txdbFile <- system.file("extdata", "hg19_knownGene_sample.sqlite",
 package = "GenomicFeatures")
 cagePath <- system.file("extdata", "cage-seq-heart.bed.bgz",
 package = "ORFik")
 reassignTxDbByCage(txdbFile, cagePath)
 
## End(Not run)

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