Asgene: AsgeneDB: A curated orthology arsenic metabolism gene...

In XinweiSong/Asgene: Rapid and accurate arsenic metabolic metagenomic analysis

AsgeneDB: A curated orthology arsenic metabolism gene database and computational tool for metagenome annotation

Description

A manually curated arsenic functional gene database (AsgeneDB) and R package (Asgene package) are developed for rapid and accurate metagenomic analysis.

Usage

Asgene(
  analysis = "abundance",
  workdir = "./",
  method = "diamond",
  toolpath = "./",
  search_parameters = "-e 1e-4 -p 28 --query-cover 80 --id 50",
  seqtype = "nucl",
  filetype = "fasta",
  PE = TRUE,
  output = "./",
  test.data = FALSE
)

Arguments

analysis	Choose the target you want to analyze,abundance or taxonomy; type = "character"; default = "abundance"
workdir	Specify directory for sequence file location;type = "character"; default = "./"
method	Specify the database searching tool you plan to use, currently diamond, usearch and blast are supported; type = "character"; default = "diamond"
toolpath	Specify directory for searching tool location; type = "character"; default = "./"
search_parameters	Define metagenomic comparison parameters; type = "character"; default = "-e 1e-4 -p 28 –query-cover 80 –id 50"
seqtype	Specify your sequence type, nucl or prot; type = "character"; default = "nucl"
filetype	Specify the extensions of your sequence files, e.g., fastq, fastq.gz, fasta,fasta.gz, fq, fq.gz, fa, fa.gz; type = "character"; default = "fasta"
PE	Specifies whether your metagenomic data were PE files, noting that PE files are named "_R1 with extension" or "_R2 with extension" (e.g., XINWEI_R1.fasta and XINWEI_R2.fasta); type = "logical"; default = TRUE
output	Specify the directory for the final result file; type = "character"; default = "./"
test.data	Example datasets are provided as input and output to help users better understand this package; type = "logical"; default = FALSE

Value

merge.data1

Examples

library(Asgene)
Asgene(analysis = "abundance", workdir = "./", method = "diamond", toolpath = "./", search_parameters = "-e 1e-4 -p 28 --query-cover 80 --id 50", seqtype = "nucl", filetype = "fasta", PE = TRUE, out = "./", test.data = FALSE)
Asgene(analysis = "abundance", workdir = "./", method = "diamond", toolpath = "./", search_parameters = "-e 1e-4 -p 28 --query-cover 80 --id 50",seqtype = "prot", output = "./", test.data = TRUE)

XinweiSong/Asgene documentation built on Sept. 20, 2022, 11:45 a.m.