odseq_unaligned: Outlier detection provided a distance/similarity matrix of...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/odseq_unaligned.R

Description

Provided a similarity matrix (like the ones provided using string kernels in kebabs). It will then compute a score for each sequence and perform bootstrap to provide information on the distribution of the scores, which is used to distinguish outlier sequences.

Usage

1
odseq_unaligned(distance_matrix, B = 100, threshold = 0.025, type = "similarity")

Arguments

distance_matrix

A numeric matrix representing either similarity or distance among unaligned sequences. Package kebabs may be useful for this task.

B

Integer indicating the number of bootstrap replicates to be run. The higher the more robust the detection should be.

threshold

Float indicating the probability to be left at the right of the bootstrap scores distribution when computing outliers. This parameter may need some tuning depending on each specific problem

type

A string indicating the type of distance metric used. Either 'similarity' or 'distance'.

Value

Returns a logical vector, where TRUE indicates an outlier.

Author(s)

Jos<c3><a9> Jim<c3><a9>nez <[email protected]>

References

[1] OD-seq: outlier detection in multiple sequence alignments. Peter Jehl, Fabian Sievers and Desmond G. Higgins. BMC Bioinformatics. 2015.

See Also

odseq

Examples

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library(kebabs)
data(seqs)
sp <- spectrumKernel(k = 3)
mat <- getKernelMatrix(sp, seqs)
odseq_unaligned(mat, B = 1000, threshold = 0.025, type = "similarity")

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, cbind, colMeans, colSums, colnames, 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: kernlab

Attaching package: 'kernlab'

The following object is masked from 'package:Biostrings':

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odseq documentation built on May 6, 2019, 2:16 a.m.