MCSCanX provides a clustering module for viewing the relationship of collinear segments in multiple genomes (or heavily redundant genomes). It takes the predicted pairwise segments from dynamic programming (DAGchainer in particular) and then tries to build consensus segments from a set of related, overlapping segments.
Usage
rcpp_mcscanx_file(
blast_file,
gff_file,
prefix = "out",
outdir = "",
match_score = 50L,
gap_penalty = -1L,
match_size = 5L,
e_value = 1e-05,
max_gaps = 25L,
overlap_window = 5L,
is_pairwise = FALSE,
in_synteny = 0L,
species_id_length = 3L,
verbose = FALSE
)Arguments
- blast_file
Character indicating the path to the BLAST/DIAMOND output file.
- gff_file
Character indicating the path to the "gff" file, which is a tab-delimited file with 4 columns indicating the chromosome name, gene id, gene start position, and gene end position, respectively.
- prefix
Character indicating the prefix to output files. Default: "out".
- outdir
Character indicating the path to the output directory. Default: "".
- match_score
Numeric indicating the match score. Default: 50.
- gap_penalty
Numeric indicating the gap penalty. Default: -1.
- match_size
Numeric indicating the minimum number of genes required to call synteny. Default: 5.
- e_value
Numeric indicating the minimum e-value allowed. Default: 1e-5.
- max_gaps
Numeric indicating the maximum number of gaps between genes allowed. The unit measure of gaps is number of genes, so
max_gaps = 20indicates that a maximum of 20 genes can exist between two homologous genes for synteny to be called. Default: 25.- overlap_window
Numeric indicating the overlap window. Default: 5.
- is_pairwise
Logical indicating whether only pairwise blocks should be reported. Default: FALSE.
- in_synteny
Numeric indicating the patterns of collinear blocks, where 0 indicates intra and interspecies comparisons, 1 indicates intraspecies comparisons, and 2 indicates interspecies comparisons. Default: 0.
- species_id_length
Integer indicating the length of the species IDs. Default: 3. 0: intra- and inter-species (default); 1: intra-species; 2: inter-species
- verbose
Logical indicating whether to print progress messages to the screen. Default: FALSE.