Infer synteny network

Usage

infer_syntenet(
  blast_list = NULL,
  annotation = NULL,
  outdir = tempdir(),
  anchors = 5,
  max_gaps = 25,
  is_pairwise = TRUE,
  verbose = FALSE,
  bp_param = BiocParallel::SerialParam(),
  ...
)

Arguments

blast_list: A list of data frames, each data frame having the tabular output of BLASTp or similar programs, such as DIAMOND. This is the output of the function run_diamond(). If you performed pairwise comparisons on the command line, you can read the tabular output as data frames and combine them in a list. List names must be have species names separated by underscore. For instance, if the first list element is a data frame containing the comparison of speciesA (query) against speciesB (database), its name must be "speciesA_speciesB".
annotation: A processed GRangesList, CompressedGRangesList, or list of GRanges as returned by process_input().
outdir: Path to the output directory. Default: tempdir().
anchors: Numeric indicating the minimum required number of genes to call a syntenic block. Default: 5.
max_gaps: Numeric indicating the number of upstream and downstream genes to search for anchors. Default: 25.
is_pairwise: specify if only pairwise blocks should be reported Default: TRUE
verbose: Logical indicating if log messages should be printed on screen. Default: FALSE.
bp_param: BiocParallel back-end to be used. Default: BiocParallel::SerialParam().
...: Any additional arguments to the MCScanX algorithm. For a complete list of all available options, see the man page of rcpp_mcscanx_file().

Value

A network represented as an edge list.

Examples

# Load data
data(proteomes)
data(annotation)
data(blast_list)

# Create processed annotation list
annotation <- process_input(proteomes, annotation)$annotation

# Infer the synteny network
net <- infer_syntenet(blast_list, annotation)