I have a dataframe with putative alignments of thousands of probe sequences. I would like to pull out the adjacent nucleotide from the genome for each alignment. My dataframe includes
seq.name for the target chromosome and I've added an
adjacent_pos variable with the location on the target chromosome that I want. Using
read.fasta from the phylotools package gives me a genome in the format of a dataframe with
seq.text for each chromosome and unplaced scaffold.
Working on a test data set with a single chromosome, I successfully used something like this:
adj <- cbind(alignments$adjacent_pos, alignments$adjacent_pos) alignments$adjacent_base <- str_sub(genome$seq.text, adj)
Now back to the whole genome, I can't wrap my head around how to direct
str_sub to the correct
seq.name for each
seq.position. I'm sure there's an elegant solution, but I haven't been able to find it!