uniqueCleavageEvents {GUIDEseq} | R Documentation

## example unique cleavage sites

### Description

An example data set containing cleavage sites with unique UMI, generated from getUniqueCleavageEvents

### Usage

    data("uniqueCleavageEvents")

### Value

cleavage.gr

  Cleavage sites with one site per UMI as GRanges with metadata column total set to 1 for each range

unique.umi.plus.R2

  a data frame containing unique cleavage site from R2 reads mapped to plus strand with the following columns chr.y (chromosome of readSide.y/R2 read) chr.x (chromosome of readSide.x/R1 read) strand.y (strand of readSide.y/R2 read) strand.x (strand of readSide.x/R1 read) start.y (start of readSide.y/R2 read) end.x (start of readSide.x/R1 read) UMI (unique molecular identifier (umi) or umi with the first few bases of R1 read)

unique.umi.minus.R2

  a data frame containing unique cleavage site from R2 reads mapped to minus strand with the following columns chr.y (chromosome of readSide.y/R2 read) chr.x (chromosome of readSide.x/R1 read) strand.y (strand of readSide.y/R2 read) strand.x (strand of readSide.x/R1 read) end.y (end of readSide.y/R2 read) start.x (start of readSide.x/R1 read) UMI (unique molecular identifier (umi) or umi with the first few bases of R1 read)

unique.umi.plus.R1

  a data frame containing unique cleavage site from R1 reads mapped to minus strand without corresponding R2 reads mapped to the plus strand, with the following columns chr.y (chromosome of readSide.y/R2 read) chr.x (chromosome of readSide.x/R1 read) strand.y (strand of readSide.y/R2 read) strand.x (strand of readSide.x/R1 read) start.x (start of readSide.x/R1 read) start.y (start of readSide.y/R2 read) UMI (unique molecular identifier (umi) or umi with the first few bases of R1 read)

unique.umi.minus.R1

  a data frame containing unique cleavage site from R1 reads mapped to plus strand without corresponding R2 reads mapped to the minus strand, with the following columns chr.y (chromosome of readSide.y/R2 read) chr.x (chromosome of readSide.x/R1 read) strand.y (strand of readSide.y/R2 read) strand.x (strand of readSide.x/R1 read) end.x (end of readSide.x/R1 read) end.y (end of readSide.y/R2 read) UMI (unique molecular identifier (umi) or umi with the first few bases of R1 read)

all.umi

  a data frame containing all the mapped reads with the following columns. readName (read ID), chr.x (chromosome of readSide.x/R1 read), start.x (start of eadSide.x/R1 read), end.x (end of eadSide.x/R1 read), mapping.qual.x (mapping quality of readSide.x/R1 read), strand.x (strand of readSide.x/R1 read), cigar.x (CIGAR of readSide.x/R1 read) , readSide.x (1/R1), chr.y (chromosome of readSide.y/R2 read) start.y (start of readSide.y/R2 read), end.y (end of readSide.y/R2 read), mapping.qual.y (mapping quality of readSide.y/R2 read), strand.y (strand of readSide.y/R2 read), cigar.y (CIGAR of readSide.y/R2 read), readSide.y (2/R2) R1.base.kept (retained R1 length), R2.base.kept (retained R2 length), distance (distance between mapped R1 and R2), UMI (unique molecular identifier (umi) or umi with the first few bases of R1 read)

### Source

http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1695644

### Examples

        data(uniqueCleavageEvents)
        names(uniqueCleavageEvents)
        sapply(uniqueCleavageEvents, class)
        uniqueCleavageEvents[[1]]  # GRanges object
        lapply(uniqueCleavageEvents, dim)

[Package GUIDEseq version 1.12.1 Index]