Basic question regarding for loop and adding each iteration to new column

2021.09.19 01:54 Darkblade48 Basic question regarding for loop and adding each iteration to new column

Hi there everyone, I have a seemingly basic question that I can't seem to wrap my head around.
As you can see from the code below, I just have a nested for loop that iterates through i and j, and parses all the possible permutations (e.g. in the case below, a combination of 1-1, 1-2, 1-3, 2-1, 2-2, 2-3, 3-1, 3-2, 3-3, etc). Of course this is a basic example that will later be expanded to a much larger data set.
Within the loop, I want to save the output (the function 'pairwiseAlignment' prints out a score that compares the strings), but right now, it's row binding each score, which is fine, but I'd prefer to have a data frame were each i iteration is a new column, while the j iteration is a new row.
I thought naively I could do it just by adding a new column via data$newcolumn, but that doesn't seem to print the new i iterations into a new column.
Any guidance would be greatly appreciated (and sorry for the long post!)
`# Load libraries library(Biostrings)
Sequences seq1 = "TGAGGAATATTGGTCAATGGACGCAAGTCTGAACCAGCCATGCCGCGTGCAGGAAGACGGCTCTATGAGTTGTAAACTGCTTTTGTACGAGGGTAAACTCACCTACGTGTAGGTGACTGAAAGTATCGTACGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGATAAGTTAGAGGTGAAATCCCGGGGCTTAACTCCGGAACTGCCTCTAATACTGTTAGACTAGAGAGTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCTTAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTATATCTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG" seq2 = "TGAGGAATATTGGTCAATGGACGAGAGTCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTATGGGTTGTAAACTTCTTTTATACGGGAATAAAGTGAGGCACGTGTGCCTTTTTGTATGTACCGTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGCGGACGCTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGGTGTCTTGAGTACAGTAGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTTGCTGGACTGTAACTGACGCTGATGCTCGAAAGTGTGGGTATCAAACAGG" seq3 = "TGGGGGATATTGCGCAATGGGGGCAACCCTGACGCAGCAACGCCGCGTGAAGGATGAAGGTTTTCGGATTGTAAACTTCTTTTATTAAGGACGAAAAATGACGGTACTTAATGAATAAGCTCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGAGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGATGTGAAATCTATGGGCTCAACCCATAAACTGCATTTGAAACTGTAGAGCTTGAGTGAAGTAGAGGCAGGCGGAATTCCCCGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTTTAACTGACGCTGAGGCACGAAAGCGTGGGTAGCAAACAGG"
Combine as set combinedseq = DNAStringSet(c(seq1, seq2, seq3))
combinedquery = combinedseq
Single alignments pairwiseAlignment(combinedseq[[1]], combinedquery[[1]], scoreOnly = TRUE) pairwiseAlignment(combinedseq[[1]], combinedquery[[2]], scoreOnly = TRUE) pairwiseAlignment(combinedseq[[1]], combinedquery[[3]], scoreOnly = TRUE)
pairwiseAlignment(combinedseq[[2]], combinedquery[[1]], scoreOnly = TRUE) pairwiseAlignment(combinedseq[[2]], combinedquery[[2]], scoreOnly = TRUE) pairwiseAlignment(combinedseq[[2]], combinedquery[[3]], scoreOnly = TRUE)
Etc Nested for loops Initialize data data = as.data.frame(NULL)
Loop for (i in 1:3){ for (j in 1:3){ data = rbind(data, ((pairwiseAlignment(combinedseq[[i]], combinedquery[[j]], scoreOnly = TRUE)))) data$new = j } }
`
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Cheering those of you on who are in the trenches.
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