exCon: Evaluation of sequence contamination

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

View source: R/exCon.R

Description

Functions for highlighting sequences that may represent external (exCon) or internal contamination (inCon).

Usage

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exCon(DNAbin, outlierLabels = "index")

inCon(DNAbin)

Arguments

DNAbin

An object of class DNAbin

outlierLabels

The format of displaying the labels of the outlying sequences. Three options are implemented: index (the default) shows the number of the outlying sequence. name shows the name of the sequence. none suppresses labelling.

Details

exCon calculates the mean distances between sequences in the alignment, systematically leaving removing a single sequence.

inCon creates a binary distance matrix that

Value

exCon plots the mean distance and 95% limits, and returns a list with the following elements:

means

Mean distance of each of the jacknifed alignments.

highCI

Upper 95% limit.

lowCI

Lower 95% limit.

above

Index of sequences above the upper limit.

below

Index of sequences below the lower limit.

inCon returns a binary matrix with 0 indicating identical sequences.

Author(s)

Samuel Brown <s_d_j_brown@hotmail.com>

See Also

ccf

Examples

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data(carpophilus)
exCon(carpoCOI)


inCon(carpoITS)

#A method of visualising the results
image(inCon(carpoITS))

carpoITSsspp <- sapply(strsplit(dimnames(carpoITS)[[1]], split = "\\|"), function(xx) xx[2])
carpoITSspp <- substr(carpoITSsspp, 1,  8)

heatmapSpp(inCon(carpoITS), carpoITSsspp)

spiderDev documentation built on May 2, 2019, 5:23 p.m.

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