OrientNucleotides: Orient Nucleotide Sequences
In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
View source: R/OrientNucleotides.R
Description
Orients nucleotide sequences to match the directionality and complementarity of specified reference sequences.
Usage
1
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OrientNucleotides(myXStringSet,
reference = which.max(width(myXStringSet)),
type = "sequences",
orientation = "all",
threshold = 0.05,
verbose = TRUE,
processors = 1)
Arguments
myXStringSet
A DNAStringSet or RNAStringSet of unaligned sequences.
reference
The index of reference sequences with the same (desired) orientation. By default the first sequence with maximum width will be used.
type
Character string indicating the type of results desired. This should be (an abbreviation of) either "sequences", "orientations", or "both".
orientation
Character string(s) indicating the allowed reorientation(s) of non-reference sequences. This should be (an abbreviation of) either "all", "reverse", "complement", and/or "both" (for reverse complement).
threshold
Numeric giving the decrease in k-mer distance required to adopt the alternative orientation.
verbose
Logical indicating whether to display progress.
processors
The number of processors to use, or NULL to automatically detect and use all available processors.
Details
Biological sequences can sometimes have inconsistent orientation that interferes with their analysis. OrientNucleotides will reorient sequences by changing their directionality and/or complementarity to match specified reference sequences in the same set. The process works by finding the k-mer distance between the reference sequence(s) and each allowed orientation of the sequences. Alternative orientations that lessen the distance by at least threshold are adopted. Note that this procedure requires a moderately similar reference sequence be available for each sequence that needs to be reoriented. Sequences for which a corresponding reference is unavailable will most likely be left alone because alternative orientations will not pass the threshold. For this reason, it is recommended to specify several markedly different sequences as references.
Value
OrientNucleotides can return two types of results: the relative orientations of sequences and/or the reoriented sequences. If type is "sequences" (the default) then the reoriented sequences are returned. If type is "orientations" then a character vector is returned that specifies whether sequences were reversed ("r"), complemented ("c"), reversed complemented ("rc"), or in the same orientation ("") as the reference sequences (marked by NA). If type is "both" then the output is a list with the first component containing the "orientations" and the second component containing the "sequences".
Author(s)
Erik Wright eswright@pitt.edu
See Also
Examples
1
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db <- system.file("extdata", "Bacteria_175seqs.sqlite", package="DECIPHER")
dna <- SearchDB(db, remove="all")
DNA <- dna # 175 sequences
# reorient subsamples of the first 169 sequences
s <- sample(169, 30)
DNA[s] <- reverseComplement(dna[s])
s <- sample(169, 30)
DNA[s] <- reverse(dna[s])
s <- sample(169, 30)
DNA[s] <- complement(dna[s])
DNA <- OrientNucleotides(DNA, reference=170:175)
DNA==dna # all were correctly reoriented
Example output
Loading required package: Biostrings
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
Loading required package: RSQLite
Search Expression:
select row_names, sequence from _Seqs where row_names in (select row_names
from Seqs)
DNAStringSet of length: 175
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[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
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DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
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Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/OrientNucleotides.R
Description
Orients nucleotide sequences to match the directionality and complementarity of specified reference sequences.
Usage
1 2 3 4 5 6 7 | OrientNucleotides(myXStringSet,
reference = which.max(width(myXStringSet)),
type = "sequences",
orientation = "all",
threshold = 0.05,
verbose = TRUE,
processors = 1)
|
Arguments
myXStringSet |
A |
reference |
The index of reference sequences with the same (desired) orientation. By default the first sequence with maximum width will be used. |
type |
Character string indicating the type of results desired. This should be (an abbreviation of) either |
orientation |
Character string(s) indicating the allowed reorientation(s) of non-reference sequences. This should be (an abbreviation of) either |
threshold |
Numeric giving the decrease in k-mer distance required to adopt the alternative orientation. |
verbose |
Logical indicating whether to display progress. |
processors |
The number of processors to use, or |
Details
Biological sequences can sometimes have inconsistent orientation that interferes with their analysis. OrientNucleotides will reorient sequences by changing their directionality and/or complementarity to match specified reference sequences in the same set. The process works by finding the k-mer distance between the reference sequence(s) and each allowed orientation of the sequences. Alternative orientations that lessen the distance by at least threshold are adopted. Note that this procedure requires a moderately similar reference sequence be available for each sequence that needs to be reoriented. Sequences for which a corresponding reference is unavailable will most likely be left alone because alternative orientations will not pass the threshold. For this reason, it is recommended to specify several markedly different sequences as references.
Value
OrientNucleotides can return two types of results: the relative orientations of sequences and/or the reoriented sequences. If type is "sequences" (the default) then the reoriented sequences are returned. If type is "orientations" then a character vector is returned that specifies whether sequences were reversed ("r"), complemented ("c"), reversed complemented ("rc"), or in the same orientation ("") as the reference sequences (marked by NA). If type is "both" then the output is a list with the first component containing the "orientations" and the second component containing the "sequences".
Author(s)
Erik Wright eswright@pitt.edu
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | db <- system.file("extdata", "Bacteria_175seqs.sqlite", package="DECIPHER")
dna <- SearchDB(db, remove="all")
DNA <- dna # 175 sequences
# reorient subsamples of the first 169 sequences
s <- sample(169, 30)
DNA[s] <- reverseComplement(dna[s])
s <- sample(169, 30)
DNA[s] <- reverse(dna[s])
s <- sample(169, 30)
DNA[s] <- complement(dna[s])
DNA <- OrientNucleotides(DNA, reference=170:175)
DNA==dna # all were correctly reoriented
|
Example output
Loading required package: Biostrings
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
Loading required package: RSQLite
Search Expression:
select row_names, sequence from _Seqs where row_names in (select row_names
from Seqs)
DNAStringSet of length: 175
Time difference of 0.05 secs
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Time difference of 0.8 secs
[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
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[31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[76] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[91] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[106] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[121] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[136] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[151] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[166] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
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