REDseq (version 1.18.0)

example.assignedREDseq: an example assigned REDseq dataset

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) ...