assignSeq2REsite: Assign mapped sequence tags to corresponding restriction...

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

Description

Given the sequence tags aligned to a genome as a GRanges, and a map built using the buildREmap function, assignSeq2REsite first identifies RE sites that have mapped sequence tags around the cut position taking consideration of user-defined offset, sequence length and strand in the aligned sequences. These RE sites are used as seeds for assigning the remaining tags depending on which of five strategies the users select for partitioning sequences associated with multiple RE sites, i.e., unique, average,estimate, best and random.

Usage

assignSeq2REsite(input.RD, REmap.RD, cut.offset = 1, seq.length = 36, 
allowed.offset = 5, min.FragmentLength = 60, max.FragmentLength = 300,  
partitionMultipleRE = c("unique", "average", "estimate","best", "random"))

Arguments

input.RD	GRanges as mapped sequences: see example below
REmap.RD	GRanges as restriction enzyme (RE) cut site map: see example below
cut.offset	The cut offset from the start of the RE recognition sequence: index is 0 based, i.e.,1 means the RE cuts at position 2.
seq.length	Sequence length: 36 means that the sequence tags are 36-base long.
allowed.offset	Offset allowed to count for imperfect sticky end repair and primer addition.
min.FragmentLength	Minimum fragment length of the sequences size-selected for sequencing
max.FragmentLength	Maximum fragment length of the sequences size-selected for sequencing
partitionMultipleRE	The strategy for partitioning sequences associated with multiple RE sites. For strategy unique, only sequence tags that are associated with a unique RE site within the distance between min.FragmentLength and max.FragmentLength are kept for downstream analysis. For strategy average, sequence tags are partitioned equally among associated RE sites. For strategy estimate, sequence tags are partitioned among associated RE sites with a weight function, which is determined using the count distribution of the RE seed sites described in the description section above. For strategy best, sequence tags are assigned to the most probable RE sties with the same weight function as that in strategy estimate. For strategy random, the sequence tags are randomly assigned to one of the multiple associated RE sites.

Value

passed.filter	Sequences assigned to RE(s), see the example r.unique$passed.filter
notpassed.filter	Sequences not assigned to any RE, see example r.unique$notpassed.filter
mREwithDetail	Detailed assignment information for sequences associated with multiple RE sites. Only available when partitionMultipleRE is set to average or estimate, see r.estimate$mREwithDetail in the examples

Author(s)

Lihua Julie Zhu

References

1. Roberts, R.J., Restriction endonucleases. CRC Crit Rev Biochem, 1976. 4(2): p. 123-64.
2.Kessler, C. and V. Manta, Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3). Gene, 1990. 92(1-2): p. 1-248.
3. Pingoud, A., J. Alves, and R. Geiger, Restriction enzymes. Methods Mol Biol, 1993. 16: p. 107-200.

See Also

buildREMap, example.REDseq, example.map, example.assignedREDseq

Examples

	library(REDseq)
	data(example.REDseq)
	data(example.map)
	r.unique = assignSeq2REsite(example.REDseq, example.map, 
cut.offset = 1, seq.length = 36, allowed.offset = 5, 
min.FragmentLength = 60, max.FragmentLength = 300, 
partitionMultipleRE = "unique")
	r.average = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1, 
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
max.FragmentLength = 300, partitionMultipleRE = "average")
	r.random = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1, 
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
 max.FragmentLength = 300, partitionMultipleRE = "random")
	r.best = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1, 
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
 max.FragmentLength = 300, partitionMultipleRE = "best")
	r.estimate = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1, 
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
 max.FragmentLength = 300, partitionMultipleRE = "estimate")
	r.estimate$passed.filter
	r.estimate$notpassed.filter

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