Parse .collinearity files obtained with MCScan — parse

The .collinearity files can be obtained with intraspecies_synteny and interspecies_synteny, which execute a native version of the MCScan algorithm.

Usage

parse_collinearity(collinearity_paths = NULL, as = "anchors")

Arguments

collinearity_paths: Character vector of paths to .collinearity files.
as: Character specifying what to extract. One of "anchors" (default), "blocks", or "all".

Value

If as is "anchors", a data frame with variables "Anchor1", and "Anchor2". If as is "blocks", a data frame with variables "Block", "Block_score", "Chr", and "Orientation". If as is "all", a data frame with all aforementioned variables, which indicate:

Block: Numeric, synteny block ID
Block_score: Numeric, score of synteny block.
Chr: Character, query and target chromosome of the synteny block formatted as "&".
Orientation: Character, the orientation of genes within blocks, with "plus" indicating that genes are in the same direction, and "minus" indicating that genes are in opposite directions.
Anchor1: Character, gene ID of anchor 1.
Anchor2: Character, gene ID of anchor 2.

Examples

collinearity_paths <- system.file(
    "extdata", "Scerevisiae.collinearity", package = "syntenet"
)
net <- parse_collinearity(collinearity_paths)