hpgltools: A pile of (hopefully) useful R functions

xref_regions

R Documentation

If I were smart I would use an I/GRanges for this.

Description

But I was asked to get the closest feature if it is not inside one. I am not sure how to do that with a ranges. Sadly, I think it will be easier for me to just iterate over the sequence_df and query each feature on that chromosome/scaffold.

Usage

xref_regions(
  sequence_df,
  gff,
  bin_width = 600,
  feature_type = "protein_coding_gene",
  feature_start = "start",
  feature_end = "end",
  feature_strand = "strand",
  feature_chr = "seqnames",
  feature_type_column = "type",
  feature_id = "ID",
  feature_name = "description",
  name_type = NULL,
  desc_column = "description"
)

Arguments

`sequence_df`	dataframe of sequence regions of interest.
`gff`	gff annotations against which to hunt.
`bin_width`	size of the regions of interest (e.g. the amplicon size)
`feature_type`	What feature type to hunt for?
`feature_start`	Column containing the starts.
`feature_end`	Column containing the ends.
`feature_strand`	Column containing strand information.
`feature_chr`	Column containing the chromosome names.
`feature_type_column`	Column containing the feature types.
`feature_id`	Column with the IDs (coming from the gff tags).
`feature_name`	Column with the descriptive name.
`name_type`	I dont remember, I think this allows one to limit the search to a feature type.
`desc_column`	Use this column to extract full-text gene descriptions.