liftBSJcoords: LiftOver back-spliced junction coordinates

In circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

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")

circRNAprofiler documentation built on March 6, 2021, 2 a.m.