rcpp_mcscanx_file: rcpp_mcscanx_file

In almeidasilvaf/syntenet: Inference And Analysis Of Synteny Networks

rcpp_mcscanx_file

Description

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 = 20 indicates 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.

Value

NULL, and a .collinearity file is created in the directory specified in outdir.

Author(s)

Kristian K Ullrich and Fabricio Almeida-Silva

References

Wang et al. (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic acids research. 40.7, e49-e49.

Haas et al. (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics. 20.18 3643-3646.

almeidasilvaf/syntenet documentation built on March 23, 2024, 8:27 a.m.