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Detect intraspecies synteny

Source: R/utils_synteny.R
intraspecies_synteny.Rd

Detect intraspecies synteny

Usage

intraspecies_synteny(
  blast_intra = NULL,
  annotation = NULL,
  intra_dir = file.path(tempdir(), "intra"),
  anchors = 5,
  max_gaps = 25,
  is_pairwise = TRUE,
  verbose = FALSE,
  bp_param = BiocParallel::SerialParam(),
  ...
)

Arguments

blast_intra

A list of BLAST/DIAMOND data frames for intraspecies comparisons as returned by run_diamond().

annotation

A processed GRangesList or CompressedGRangesList object as returned by process_input().

intra_dir

Path to output directory where .collinearity files will be stored.

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

Logical indicating 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

Paths to .collinearity files.

Examples

# Load data
data(scerevisiae_annot)
data(scerevisiae_diamond)

# Detect intragenome synteny
intra_syn <- intraspecies_synteny(
    scerevisiae_diamond, scerevisiae_annot
)