R: Percent Identity Filter

filter.identity {bio3d} | R Documentation

## Percent Identity Filter

### Description

Identify and filter subsets of sequences at a given sequence identity cutoff.

### Usage

    filter.identity(aln = NULL, ide = NULL, cutoff = 0.6, verbose = TRUE, ...)

### Arguments

`aln` | sequence alignment list, obtained from `seqaln` or `read.fasta`, or an alignment character matrix. Not used if ‘ide’ is given.
`ide` | an optional identity matrix obtained from `seqidentity`.
`cutoff` | a numeric identity cutoff value ranging between 0 and 1.
`verbose` | logical, if TRUE print details of the clustering process.
`...` | additional arguments passed to and from functions.

### Details

This function performs hierarchical cluster analysis of a given sequence identity matrix ‘ide’, or the identity matrix calculated from a given alignment ‘aln’, to identify sequences that fall below a given identity cutoff value ‘cutoff’.

### Value

Returns a list object with components:

`ind` | indices of the sequences below the cutoff value.
`tree` | an object of class `"hclust"`, which describes the tree produced by the clustering process.
`ide` | a numeric matrix with all pairwise identity values.

### Author(s)

Barry Grant

### References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

### See Also

`read.fasta`, `seqaln`, `seqidentity`, `entropy`, `consensus`

### Examples

    attach(kinesin)

    ide.mat <- seqidentity(pdbs)

    # Histogram of pairwise identity values
    op <- par(no.readonly=TRUE)
    par(mfrow=c(2,1))
    hist(ide.mat[upper.tri(ide.mat)], breaks=30,xlim=c(0,1),
         main="Sequence Identity", xlab="Identity")

    k <- filter.identity(ide=ide.mat, cutoff=0.6)
    ide.cut <- seqidentity(pdbs$ali[k$ind,])
    hist(ide.cut[upper.tri(ide.cut)], breaks=10, xlim=c(0,1),
         main="Sequence Identity", xlab="Identity")

    #plot(k$tree, axes = FALSE, ylab="Sequence Identity")
    #print(k$ind) # selected
    par(op)
    detach(kinesin)

[Package bio3d version 2.3-3 Index]