intraspecies_synteny: Detect intraspecies synteny

In almeidasilvaf/syntenet: Inference And Analysis Of Synteny Networks

Detect intraspecies synteny

Description

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
)

almeidasilvaf/syntenet documentation built on Oct. 12, 2024, 5:51 p.m.