Coerces sequences from a sq object to
a matrix, in which rows correspond to sequences and columns to
positions.
# S3 method for sq
as.matrix(x, ...)[sq]
An object this function is applied to.
further arguments to be passed from or to other methods.
A matrix with number of rows the same as number of
sequences and number of columns corresponding to the length of the longest
sequence in the converted sq object.
This method for class sq allows converting sequences from the
sq object into a matrix. Each row corresponds to the separate sequence
from the sq object, whereas each column indicates a single position
within a sequence. Dimensions of matrix are determined by the number of
sequences (rows) and the length of the longest sequence (columns). If length
of a sequence is smaller than the length of the longest sequence, the
remaining columns are filled with NA. All attributes of the input
sq are lost during the conversion to matrix.
Functions from output module:
as.character.sq(),
as.sq(),
export_sq(),
write_fasta()
# Creating objects to work on:
sq_dna <- sq(c("CGATAGACA", "TGACAAAAC", "GTGACCGTA"),
alphabet = "dna_bsc")
sq_rna <- sq(c("CUGAAUGCAGUACCGUAAU", "AUGCCGUAAAUGCCAU", "CAGACCANNNAUAG"),
alphabet = "rna_ext")
# Sequences of the same lengths can be converted easily:
as.matrix(sq_dna)
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
#> [1,] "C" "G" "A" "T" "A" "G" "A" "C" "A"
#> [2,] "T" "G" "A" "C" "A" "A" "A" "A" "C"
#> [3,] "G" "T" "G" "A" "C" "C" "G" "T" "A"
# Sequences that differ in length are filled with NA to the maximum length:
as.matrix(sq_rna)
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
#> [1,] "C" "U" "G" "A" "A" "U" "G" "C" "A" "G" "U" "A" "C" "C"
#> [2,] "A" "U" "G" "C" "C" "G" "U" "A" "A" "A" "U" "G" "C" "C"
#> [3,] "C" "A" "G" "A" "C" "C" "A" "N" "N" "N" "A" "U" "A" "G"
#> [,15] [,16] [,17] [,18] [,19]
#> [1,] "G" "U" "A" "A" "U"
#> [2,] "A" "U" NA NA NA
#> [3,] NA NA NA NA NA