mat.dif: Matrices of difference scores between sequences

In bios2mds: From Biological Sequences to Multidimensional Scaling

Description

Computes a matrix providing the distances based on the difference scores between sequences from two multiple sequence alignments.

Usage

mat.dif(align1, align2, gap = FALSE, aa.strict = FALSE, sqrt = FALSE)

Arguments

align1	a list of character vectors representing a first multiple sequence aligment.
align2	a list of character vectors representing a second multiple sequence aligment.
gap	a logical value indicating whether gap character should be taken as supplementary symbol (TRUE) or not (FALSE). Default is FALSE.
aa.strict	a logical value indicating whether only strict amino acids should be taken into account (TRUE) or not (FALSE). To be used only for amino acid sequences. Default is FALSE.
sqrt	a logical value indicating whether the distance should be equal to the squared root of the difference score (TRUE) or not (FALSE). Default is FALSE.

Details

If align1 and align2 are identical, mat.dif computes the symetrical matrix of distances between each sequence of the alignment.

Before using mat.dif, users must check the alignment of sequences within align1 and align2 and between align1 and align2.

Value

A named numeric matrix providing the difference-based distances between each pair of sequences from align1 and align2. The number of rows and columns is identical to the number of sequences in align1 and align2, respectively.

Author(s)

Julien Pele and Jean-Michel Becu

See Also

identity function from bio3d package.

Examples

# calculating the matrix of distances based on the difference scores
# between GPCRs sample from H. sapiens and D. melanogaster:
aln_human <- import.fasta(system.file("msa/human_gpcr.fa", package = "bios2mds"))
aln_drome <- import.fasta(system.file("msa/drome_gpcr.fa", package = "bios2mds"))
mat.dif1 <- mat.dif(aln_human[1:5], aln_drome[1:5])
mat.dif1

Example output

Loading required package: amap
Loading required package: e1071
Loading required package: scales
Loading required package: cluster
Loading required package: rgl
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
            Q8MTX9_DROME Q8MU51_DROME A1KXD5_DROME A1Z6J7_DROME A1ZAX0_DROME
CLTR1_HUMAN        0.742        0.737        0.864        0.754        0.720
CLTR2_HUMAN        0.737        0.725        0.855        0.754        0.703
FFAR1_HUMAN        0.797        0.797        0.838        0.801        0.814
FFAR2_HUMAN        0.809        0.809        0.864        0.771        0.763
FFAR3_HUMAN        0.763        0.767        0.860        0.733        0.725

bios2mds documentation built on April 14, 2020, 5:08 p.m.