mmexpand_network: Find connections of a subset of scaffolds in a larger set of...

In KasperSkytte/mmgenome2: Tools for extracting individual genomes from metagenomes

Description

Searches for all connections between the given set of scaffolds and the scaffolds in mm. The given set of scaffolds is often a subset of mm, but can also be a manually selected set of scaffolds from which to find connections in mm.

Usage

mmexpand_network(
  mm,
  scaffolds,
  network,
  min_connections = 2,
  include_connections = "direct"
)

Arguments

mm	(required) A dataframe loaded with mmload in which to find connections from scaffolds.
scaffolds	(required) The scaffolds from which to find connections in mm. Must be a vector of scaffold names or a dataframe with scaffold names in the first column.
network	(required) Paired-end or mate-pair connections between scaffolds in long format. The first and second columns must contain all connected scaffold pairs and the third column the number of connections.
min_connections	Filter all scaffold pairs with equal to or less than this number of connections before the extraction. (Default: 2)
include_connections	The connections to include. One of the following: "direct" Extract only scaffolds from mm that are directly connected to any of the scaffolds in scaffolds. (default) "all" Same as "direct", except that any further connections to connected scaffolds are also included, continuing until no further connections are found.

Value

A dataframe (tibble) compatible with other mmgenome2 functions.

Author(s)

Kasper Skytte Andersen [e-mail]

Soren M. Karst [e-mail]

Mads Albertsen [e-mail]

Examples

library(mmgenome2)
data(mmgenome2)
data(paired_ends)
mmgenome2
selection <- data.frame(
  cov_C13.11.25 = c(7.2, 16.2, 25.2, 23.3, 10.1),
  cov_C14.01.09 = c(47, 77, 52.8, 29.5, 22.1)
)
mmgenome2_extraction <- mmextract(mmgenome2,
  min_length = 3000,
  selection = selection,
  inverse = FALSE
)
mmgenome2_extraction
mmgenome2_extraction_expanded <- mmexpand_network(
  mm = mmgenome2,
  scaffolds = mmgenome2_extraction,
  network = paired_ends,
  min_connections = 10,
  include_connections = "direct"
)
mmgenome2_extraction_expanded

KasperSkytte/mmgenome2 documentation built on Dec. 14, 2021, 12:11 a.m.