I'm struggling to load the BLOSUM62 matrix in R, that I know it should be inside the package Biostrings
. I'm new in R, I'm following an exercise that uses this matrix without problems, while when I try to compile I get the error
dataset not found
I tried to reinstall Biostring but I cannot fix it.
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("Biostrings")
library(Biostrings)
data("BLOSUM62")
In data("BLOSUM62") : dataset ‘BLOSUM62’ not found
I also tried to download the matrix from NCBI I load it correctly from a .txt and convert it into a 25x25 matrix
BLOSUM62=read.table("BLOSUM62.txt", header = TRUE)
BLOSUM62 <- data.matrix(BLOSUM62)
and it works, but then I should compare it with another dataset (from the exercise did it in class) I get the error
Gene <- msa(Geneseq, substitutionMatrix = "blosum", method = "ClustalW")
cs <- msaConservationScore(Gene, BLOSUM62)
Error in msaConservationScore.matrix(mat, ...) : substitution matrix is not in proper format
How can I solve it?
The matrix BLOSUM62
can be found in the pwalign
package.
library(pwalign)
data("BLOSUM62")
print(BLOSUM62)
A R N D C Q E G H I ...
A 4 -1 -2 -2 0 -1 -1 0 -2 -1 ...
R -1 5 0 -2 -3 1 0 -2 0 -3 ...
N -2 0 6 1 -3 0 0 0 1 -3 ...
D -2 -2 1 6 -3 0 2 -1 -1 -3 ...
C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 ...
Q -1 1 0 0 -3 5 2 -2 0 -3 ...
E -1 0 0 2 -4 2 5 -2 0 -3 ...
G 0 -2 0 -1 -3 -2 -2 6 -2 -4 ...
H -2 0 1 -1 -3 0 0 -2 8 -3 ...
I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 ...
...