pairToEvents: Read "pair" format of EMBOSS needle into GRanges as events.
In amplican: Automated analysis of CRISPR experiments
Description
Usage
Arguments
Value
View source: R/helpers_general.R
Description
Parse EMBOSS needle (or needleall) "pair" format into GRanges representation
with events of deletions, insertions and mismatches. Make sure that each file
corresponds to single subject (single amplicon). Assumes that bottom sequence
"-bsequence" corresponds to the "subject" and full sequence alignment is
returned.
Usage
1
pairToEvents(file, ID = "NA", strand_info = "+")
Arguments
file
(character) File path.
ID
(character) ID of the experiment, will be used as seqnames of the
reutner ranges.
strand_info
(character) Strand to assign.
Value
(GRanges) Same as events.
amplican documentation built on Nov. 8, 2020, 11:10 p.m.
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Description Usage Arguments Value
View source: R/helpers_general.R
Description
Parse EMBOSS needle (or needleall) "pair" format into GRanges representation with events of deletions, insertions and mismatches. Make sure that each file corresponds to single subject (single amplicon). Assumes that bottom sequence "-bsequence" corresponds to the "subject" and full sequence alignment is returned.
Usage
1 | pairToEvents(file, ID = "NA", strand_info = "+")
|
Arguments
file |
(character) File path. |
ID |
(character) ID of the experiment, will be used as seqnames of the reutner ranges. |
strand_info |
(character) Strand to assign. |
Value
(GRanges) Same as events.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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