Get a list of anchor pairs for each species

Usage

get_anchors_list(
  blast_list = NULL,
  annotation = NULL,
  evalue = 1e-10,
  anchors = 5,
  max_gaps = 25,
  collinearity_dir = NULL
)

Arguments

blast_list: A list of data frames containing BLAST tabular output for intraspecies comparisons. Each list element corresponds to the BLAST output for a given species, and names of list elements must match the names of list elements in annotation. BLASTp, DIAMOND or simular programs must be run on processed sequence data as returned by process_input().
annotation: A processed GRangesList or CompressedGRangesList object as returned by syntenet::process_input().
evalue: Numeric scalar indicating the E-value threshold. Default: 1e-10.
anchors: Numeric indicating the minimum required number of genes to call a syntenic block, as in syntenet::infer_syntenet. Default: 5.
max_gaps: Numeric indicating the number of upstream and downstream genes to search for anchors, as in syntenet::infer_syntenet. Default: 25.
collinearity_dir: Character indicating the path to the directory where .collinearity files will be stored. If NULL, files will be stored in a subdirectory of tempdir(). Default: NULL.

Value

A list of data frames representing intraspecies anchor pairs.

Examples

data(diamond_intra)
data(yeast_annot)
data(yeast_seq)
blast_list <- diamond_intra

# Get processed annotation for S. cerevisiae
annotation <- syntenet::process_input(yeast_seq, yeast_annot)$annotation
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.integer()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.integer()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead

# Get list of intraspecies anchor pairs
anchorpairs <- get_anchors_list(blast_list, annotation)