liftBSJcoords {circRNAprofiler} | R Documentation

## LiftOver back-spliced junction coordinates

### Description

The function liftBSJcoords() maps back-spliced junction coordinates between species ad genome assemblies by using the liftOver utility from UCSC. Only back-spliced junction coordinates where the mapping was successful are reported.

### Usage

    liftBSJcoords(
      backSplicedJunctions,
      map = "hg19ToMm9",
      annotationHubID = "AH14155"
    )

### Arguments

`backSplicedJunctions` | A data frame containing the back-spliced junction coordinates (predicted or randomly selected). See `getRandomBSJunctions`, `getBackSplicedJunctions` and `mergeBSJunctions` (to group circRNAs detected by multiple detection tools), on how to generated this data frame.
`map` | A character string in the format <db1>To<Db2> (e.g."hg19ToMm9") specifying the reference genome mapping logic associated with a valid .chain file. Default value is "hg19ToMm9".
`annotationHubID` | A string specifying the AnnotationHub id associated with a valid *.chain file. Type data(ahChainFiles) to see all possibile options. E.g. if AH14155 is specified, the hg19ToMm9.over.chain.gz will be used to convert the hg19 (Human GRCh37) coordinates to mm10 (Mouse GRCm38). Default value is "AH14155".

### Value

a data frame.

### Examples

    # Load a data frame containing detected back-spliced junctions
    data("mergedBSJunctions")

    # LiftOver the first 10 back-spliced junction coordinates
    liftedBSJcoords <- liftBSJcoords(mergedBSJunctions[1:10,], map = "hg19ToMm9")

[Package circRNAprofiler version 1.4.2 Index]