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TheAlgorithms / R

Collection of various algorithms implemented in R.
MIT License
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MSA problem in R Studio #94

Open oliver7423 opened 1 year ago

oliver7423 commented 1 year ago

Hi! I'm working for my midterms and I need answers ASAP

I downloaded sequences from NCBI (Complete Record > Fasta) and I installed necessary packages. By the time I reached using msa, the error appears. I don't know what to do anymore. Help! This is the codes by the way.

AlignNeeded = TRUE # The program reads fasta file and aligns it if (AlignNeeded) {

file <- readDNAStringSet(fname)#for reading multiple DNA sequences from msa package file }

cb<- msa(file) # multiple sequence alignment from msa package cb # aligned the 120 sequences in the file

use default substitution matrix Error in convertAlnRows(result$msa, type) : There is an invalid aln file!

AFTER READING A SOLUTION HERE, I TRIED IT OUT, HERE'S THE PROBLEM

cb<- msa(file) # multiple sequence alignment from msa package use default substitution matrix Error in convertAlnRows(result$msa, type) : There is an invalid aln file! library(Biostrings) file_path <- "sequence-5.fasta" cb <- msa(file_path, filetype = "sequence-5.fasta", type = "DNA") Error in msaFun(inputSeqs = inputSeqs, cluster = cluster, gapOpening = gapOpening, : The following parameters are not known (or have been specifiedmore often than once): filetype

PLEASE HELP ME

oliver7423 commented 1 year ago

im good. i just needed an aligned file.