Forum: help

dist.matrix is producing multiple distance matrices, I only want one [ Reply ]
By: Su M on 2017-04-26 10:50

I'm new to R and I have the following: a concatenated fasta file and I want to compute the distance matrix. I'm running my script via sbatch. My R script is:
library(seqinr)
args = commandArgs(trailingOnly=TRUE)
if(length(args)==0){
print("No arguments supplied.")
}

myseqs <- read.alignment(file=args, format = "fasta")
dist.alignment(myseqs, matrix = "identity")
m<-as.matrix(dist.alignment(myseqs, matrix = "identity"))

write.matrix(m, file = "", sep = " ", blocksize)

I get rows omitted error so I added:

options(max.print=500000)

But I still get rows omitted error. In addition, the distance matrix is being computed multiple times and is outputting multiple matrices. Does anyone know how to produce one matrix only.