uniqueCleavageEvents:
example unique cleavage sites
Description
An example data set containing cleavage sites with unique UMI, generated from
getUniqueCleavageEvents
Usage
data("uniqueCleavageEvents")
Arguments
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)