Description Usage Arguments Value Examples
View source: R/hub_seqs_exclusion.R
Deletes top hub sequences from repertoire, changing the network architecture.
1 2 | hub_seqs_exclusion(repertoire, top_x = 0.005, report = FALSE,
output_dir = "", verbose = TRUE)
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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) |
Repertoire reduced by hub sequence (new network architecture)
1 2 | repertoire <- list_example_repertoires[["example_repertoire_A"]]
rep_excluded_hubs <- hub_seqs_exclusion(repertoire, top_x = 0.005, output_dir = "")
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