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

In immuneSIM: Tunable Simulation of B- And T-Cell Receptor Repertoires

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

repertoire <- list_example_repertoires[["example_repertoire_A"]]
rep_excluded_hubs <- hub_seqs_exclusion(repertoire, top_x = 0.005, output_dir = "")

immuneSIM documentation built on Sept. 27, 2019, 5:02 p.m.