Example FASTA.

example.fasta

>seq1
GGGGGTCGAGACCCCAGCCACAAAGGTAACGCACATGTGAACGGGCCCCG

Example ranges.

ranges <- data.frame(V1=c(10, 25), strand=rep("-", 2))

With sequences in R you usually want to work with them as a Biostrings object.

library("Biostrings")

fasta <- readDNAStringSet("example.fasta")

> fasta
DNAStringSet object of length 1:
    width seq                                               names               
[1]    50 GGGGGTCGAGACCCCAGCCACAA...AACGCACATGTGAACGGGCCCCG seq1

Ranges in R should normally be stored as GRanges objects.

library("GenomicRanges")

ranges$seqnames <- "seq1"
ranges <- makeGRangesFromDataFrame(ranges, start.field="V1", end.field="V1")

> ranges
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     seq1        10      -
  [2]     seq1        25      -
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

You can then easily manipulate the ranges to the desired widths. Here I'll extend it 5 bases downstream and 10 bases upstream.

start(ranges) <- start(ranges) - 5
end(ranges) <- end(ranges) + 10

> ranges
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     seq1      5-20      -
  [2]     seq1     20-35      -
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

Extracting the sequences are now simple.

library("BSgenome")

> getSeq(fasta, ranges)
DNAStringSet object of length 2:
    width seq
[1]    16 TGGCTGGGGTCTCGAC
[2]    16 TGTGCGTTACCTTTGT