Plot matches as alignments against target sequence feature

Usage

plotAlignment(
  match.info,
  guide.seq,
  seqs,
  aln.name = "alignment",
  left.pad = 0,
  right.pad = 0,
  seq.start.pos = 2,
  seq.stop.pos = 8,
  output.type = c("data.frame", "ggplot")
)

Arguments

match.info: A row from the data.frame of matches produced by SeedMatchR
guide.seq: The full siRNA guide sequence
seqs: The feature sequences used in scanning
aln.name: The column name for the data.frame reporting alignments
left.pad: The number of nucleotides to the left to show on the feature sequence beyond the length of the guide sequence.
right.pad: The number of nucleotides to the right to show on the feature sequence beyond the length of the guide sequence.
seq.start.pos: The seed definition start position
seq.stop.pos: The seed definition stop position
output.type: Either data.frame or ggplot

Value

A data.frame representing the input sequences and alignment between them.