assignTSSByCage {ORFik} | R Documentation

## Input a txdb and add a 5' leader for each transcript, that does not have one.

### Description

For all cds in txdb, that does not have a 5' leader: Start at 1 base upstream of cds and use CAGE, to assign leader start. All these leaders will be 1 exon based, if you really want exon splits, you can use exon prediction tools, or run sequencing experiments.

### Usage

    assignTSSByCage(txdb, cage, extension = 1000, filterValue = 1,
      restrictUpstreamToTx = FALSE)

### Arguments

`txdb` | a TxDb object, normally from a gtf file.
`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.
`restrictUpstreamToTx` | a logical (FALSE), if you want to restrict leaders to not extend closer than 5 bases from closest upstream leader, set this to TRUE.

### Details

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).

### Value

a TxDb obect of reassigned transcripts

### See Also

Other CAGE: `reassignTSSbyCage`, `reassignTxDbByCage`

### Examples

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

    ## End(Not run)

[Package ORFik version 1.2.1 Index]