example.assignedREDseq: an example assigned REDseq dataset

In REDseq: Analysis of high-throughput sequencing data processed by restriction enzyme digestion

Description

an example assigned REDseq dataset generated from assignSeq2REsite

Usage

data(example.assignedREDseq)

Format

The format is: List of 3
$ passed.filter :'data.frame': Sequences that passed the filters:
..$ SEQid :Sequence ID
..$ REid : Restriction Enzyme Site ID
..$ Chr : Chromosome
..$ strand : Strand
..$ SEQstart: Sequence Start
..$ SEQend : Sequence End
..$ REstart : Restriction Enzyme Site Start
..$ REend : Restriction Enzyme Site End
..$ Distance: Distance from SEQstart to REstart
..$ Weight : Weighted count for this REid and this SEQid
$ notpassed.filter:'data.frame' : Sequences that did not pass the filters
..$ SEQid :Sequence ID
..$ REid : Restriction Enzyme Site ID
..$ Chr : Chromosome
..$ strand : Strand
..$ SEQstart: Sequence Start
..$ SEQend : Sequence End
..$ REstart : Restriction Enzyme Site Start
..$ REend : Restriction Enzyme Site End
..$ Distance: Distance from SEQstart to REstart
..$ Weight : Weighted count for this REid and this SEQid
$ mREwithDetail :'data.frame': Detailed information about the sequences that are associated with multiple REid - for debugging:
..$ SEQid :Sequence ID
..$ REid : Restriction Enzyme Site ID
..$ Chr : Chromosome
..$ strand : Strand
..$ SEQstart: Sequence Start
..$ SEQend : Sequence End
..$ REstart : Restriction Enzyme Site Start
..$ REend : Restriction Enzyme Site End
..$ Distance: Distance from SEQstart to REstart
..$ Weight : Weighted count for this REid and this SEQid
..$ count : count of seed for this REid and SEQid
..$ total.count: total number of seeds that are associated with this SEQid

Examples

library(REDseq)
data(example.assignedREDseq)
## maybe str(example.assignedREDseq) ; plot(example.assignedREDseq) ...

REDseq documentation built on Nov. 8, 2020, 8:19 p.m.