View source: R/roary_2_pagoo.R
roary_2_pagoo | R Documentation |
This function handle conversion of roary's output files into
a pagoo R6 class object. It takes the "gene_presence_absence.csv" file and
(optionally but recommended) gff input file paths, and returns an object of
class PgR6MS
(or PgR6M
if left
empty the gffs
argument).
roary_2_pagoo(gene_presence_absence_csv, gffs, sep = "__", paralog_sep = "\t")
gene_presence_absence_csv |
|
gffs |
A |
sep |
|
paralog_sep |
|
A pagoo's R6 class object. Either PgR6M, if gffs
argument is left empty, or PgR6MS if path to gff files is
provided.
Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015;31(22):3691-3693
## Not run: gffs <- list.files(path = "path/to/gffs/", pattern = "[.]gff$", full.names = TRUE) gpa_csv <- "path/to/gene_presence_absence.csv" library(pagoo) pg <- roary_2_pagoo(gene_presence_absence_csv = gpa_csv, gffs = gffs) ## End(Not run)
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