sequence retrieval in R using fasta file

Question

[rsabrina93]

I have a Hg19.fasta file and I have a csv file which contains the genomic coordinates of all 23 chromosomes which the sequence is to be retrieved. How can I do it using R?

[WouterDeCoster]

Not what you ask for, but bedtools getfasta would be the way to do this if you wouldn't constrain to R.

Answer 1

[Jean-Karim Heriche]

You could use the R package seqinr to read the FASTA file with read.fasta(), read the csv file with read.csv() then subset the sequence using the coordinates. There may also be something for you in the Bioconductor GenomicRanges package.