join_bgc_gff: Reads in BGC Outlier Data and Joins with GFF Data

View source: R/join_bgc_gff.R

join_bgc_gffR Documentation

Reads in BGC Outlier Data and Joins with GFF Data

Description

This function joins BGC outlier data with info from a GFF file. It outputs a joined data.frame of BGC loci that match to GFF genes. The BGC outlier loci names must be GenBank transcript IDs that can be related to the transcript IDs in the GFF file The BGC outlier object must also be generated using upstream methods. See ?get_bgc_outliers for more info. Read In BGC Data and Join With GFF Annotations

Usage

join_bgc_gff(prefix, outlier.list, gff.data, scafInfoDIR = "./scaffold_info")

Arguments

prefix

Prefix for output file

outlier.list

List generated from get_bgc_outliers(). See ?get_bgc_outliers.

gff.data

Object output from read_parse_GFF(). See ?read_parse_GFF

scafInfoDIR

Directory to save output from this function.

Value

Data.frame containing outliers genes joined with GFF data

Examples

outlier.genes <- join_bgc_gff(prefix = "population1",
                              outlier.list = outliers,
                              gff.data = gff.df,
                              scafInfoDIR = "./scaffold_info")

btmartin721/ClineHelpR documentation built on Oct. 15, 2024, 5:05 a.m.