reformat.syntenyData: Reformat synteny data

In marta-fb/syntenyPlotteR: Genome Synteny Visualization

Reformat synteny data

Description

Reformat synteny data

Usage

reformat.syntenyData(
  file_data,
  filename,
  directory = NULL,
  reference.species = reference.sps,
  target.species = target.sps
)

Arguments

file_data	input file name for descrambler .map data
filename	output file name for reformatted data
directory	string containing file path to chosen directory to save text file
reference.species	reference species identifier as a character string
target.species	target species identifier as a character string

Details

This function takes output from alignment softwares such as deschrambler and inferCARs and re-formats it for syntenyPlotteR - this does not curate files only re-formats it

It requires as input:

1. The data output from deschrambler or inferCARs

2. the desired output file name

There are optional parameters for some customization of this function:

1. reference.species allows you to set the reference species identifier that will be set in the final output table i.e. reference.species = "ref"

2. target.species allows you to set the target species identifier that will be set in the final output table i.e. target.species = "tar"

3. The directory where the text file should be saved, as default the file is saved to temporary directory, change by inputting: directory = "path/to/directory"

Example: reformat.syntenyData("deschrambler.output", "reformatted.data", directory = "path/to/directory", reference.species = "ref", target.species = "tar" )

Value

A text file with the reformatted data

Examples

# Create object containing file path to external dataset
# (see vignette to follow examples with personal data)

file <- system.file("extdata", "example_map_1.map", package = "syntenyPlotteR")

# -----------------------------------------------------------------------------------

# Run reformat.syntenyData function
# To run example and save file to working directory
# add directory parameter and set working directory
# To run example with personal data see vignette

reformat.syntenyData(file, "outputName")

marta-fb/syntenyPlotteR documentation built on Jan. 25, 2024, 3:34 p.m.