mat.dif {bios2mds} | R Documentation |
Computes a matrix providing the distances based on the difference scores between sequences from two multiple sequence alignments.
mat.dif(align1, align2, gap = FALSE, aa.strict = FALSE, sqrt = FALSE)
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. |
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
.
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.
Julien Pele and Jean-Michel Becu
identity
function from bio3d
package.
# 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