Description Usage Arguments Value Author(s) See Also Examples

The `trimLRPatterns`

function trims left and/or right flanking patterns
from sequences.

1 2 3 4 |

`Lpattern` |
The left pattern. |

`Rpattern` |
The right pattern. |

`subject` |
An XString object, XStringSet object, or character vector containing the target sequence(s). |

`max.Lmismatch` |
Either an integer vector of length When Otherwise, Once the integer vector is constructed using the rules given above, when
For a given element |

`max.Rmismatch` |
Same as For a given element |

`with.Lindels` |
If |

`with.Rindels` |
Same as |

`Lfixed, Rfixed` |
Whether IUPAC extended letters in the left or right pattern should
be interpreted as ambiguities (see |

`ranges` |
If |

A new XString object, XStringSet object, or character vector with the "longest" flanking matches removed, as described above.

P. Aboyoun and H. Jaffee

`matchPattern`

,
`matchLRPatterns`

,
lowlevel-matching,
XString-class,
XStringSet-class

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ```
Lpattern <- "TTCTGCTTG"
Rpattern <- "GATCGGAAG"
subject <- DNAString("TTCTGCTTGACGTGATCGGA")
subjectSet <- DNAStringSet(c("TGCTTGACGGCAGATCGG", "TTCTGCTTGGATCGGAAG"))
## Only allow for perfect matches on the flanks
trimLRPatterns(Lpattern = Lpattern, subject = subject)
trimLRPatterns(Rpattern = Rpattern, subject = subject)
trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subjectSet)
## Allow for perfect matches on the flanking overlaps
trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subjectSet,
max.Lmismatch = 0, max.Rmismatch = 0)
## Allow for mismatches on the flanks
trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subject,
max.Lmismatch = 0.2, max.Rmismatch = 0.2)
maxMismatches <- as.integer(0.2 * 1:9)
maxMismatches
trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subjectSet,
max.Lmismatch = maxMismatches, max.Rmismatch = maxMismatches)
## Produce ranges that can be an input into other functions
trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subjectSet,
max.Lmismatch = 0, max.Rmismatch = 0, ranges = TRUE)
trimLRPatterns(Lpattern = Lpattern, Rpattern = Rpattern, subject = subject,
max.Lmismatch = 0.2, max.Rmismatch = 0.2, ranges = TRUE)
``` |

```
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
11-letter "DNAString" instance
seq: ACGTGATCGGA
13-letter "DNAString" instance
seq: TTCTGCTTGACGT
A DNAStringSet instance of length 2
width seq
[1] 6 ACGGCA
[2] 0
A DNAStringSet instance of length 2
width seq
[1] 6 ACGGCA
[2] 0
4-letter "DNAString" instance
seq: ACGT
[1] 0 0 0 0 1 1 1 1 1
A DNAStringSet instance of length 2
width seq
[1] 6 ACGGCA
[2] 0
IRanges object with 2 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 7 12 6
[2] 10 9 0
IRanges object with 1 range and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 10 13 4
```

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