set_syntenyParams: Set synteny parameters and parse required data

In jtlovell/GENESPACE: Synteny- and orthology-constrained comparative genomics

Set synteny parameters and parse required data

Description

set_syntenyParams Generate all data needed to run synteny. This includes the synteny parameters, combined/annotated bed file and annotated blast files.

set_syntenyParams Locate the required orthofinder results for genespace, which are stored in the /results directory. Typically for internal use. If called directly, use with caution.

find_ofFiles Find raw orthofinder results files. Typically for internal use with copy_of2results. If called directly, use with caution.

copy_of2results copy files from an orthofinder run to the genespace results directory. Typically for internal use. If called directly, use with caution.

Usage

set_syntenyParams(gsParam)

find_ofFiles(orthofinderDir)

copy_of2results(orthofinderDir, resultsDir)

Arguments

gsParam	A list of genespace parameters. This should be created by init_genespace.
orthofinderDir	file.path to the raw orthofinder directory If called, set_syntenyParams returns its own arguments.
resultsDir	file.path to the results directory

jtlovell/GENESPACE documentation built on Jan. 25, 2025, 6:39 a.m.