immuneSIM (version 0.8.7)

hub_seqs_exclusion: Deletes top hub sequences from repertoire, changing the network architecture.

Description

Deletes top hub sequences from repertoire, changing the network architecture.

Usage

hub_seqs_exclusion(repertoire, top_x = 0.005, report = FALSE,
  output_dir = "", verbose = TRUE)

Arguments

repertoire

An annotated AIRR compliant repertoire.

(http://docs.airr-community.org/en/latest/)

top_x

Determines what percentage of hub sequences get excluded

(Default: 0.005, i.e. Top 0.5 percent)

report

The user can choose to output a report csv file containing the excluded sequences. (Default: FALSE)

output_dir

If user specifies and output directory a csv file containing the excluded sequences is saved at that path, otherwise it will be saved in tempdir().

verbose

Determines whether messages on plot locations are output to user. (Default: TRUE)

Value

Repertoire reduced by hub sequence (new network architecture)

Examples

# NOT RUN {
repertoire <- list_example_repertoires[["example_repertoire_A"]]
rep_excluded_hubs <- hub_seqs_exclusion(repertoire, top_x = 0.005, output_dir = "")
# }