repFilter: Main function for data filtering

In immunarch: Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design in R

Main function for data filtering

Description

Usage

repFilter(
  .data,
  .method = "by.clonotype",
  .query = list(CDR3.aa = exclude("partial", "out_of_frame")),
  .match = "exact"
)

Arguments

.data	The data to be processed. Must be the list of 2 elements: a data table and a metadata table.
.method	Method of filtering. Implemented methods: by.meta, by.repertoire (by.rep), by.clonotype (by.cl) Default value: 'by.clonotype'.
.query	Filtering query. It's a named list of filters that will be applied to data. Possible values for names in this list are dependent on filter methods: by.meta: filters by metadata. Names in the named list are metadata column headers. by.repertoire: filters by the number of clonotypes or total number of clones in sample. Possible names in the named list are "n_clonotypes" and "n_clones". by.clonotype: filters by data in all samples. Names in the named list are data column headers. Elements of the named list for each of the filters are filtering options. Possible values for filtering options: include("STR1", "STR2", ...): keeps only rows with matching values. Available for methods: "by.meta", "by.clonotype". exclude("STR1", "STR2", ...): removes rows with matching values. Available for methods: "by.meta", "by.clonotype". lessthan(value): keeps rows/samples with numeric values less than specified. Available for methods: "by.meta", "by.repertoire", "by.clonotype". morethan(value): keeps rows/samples with numeric values more than specified. Available for methods: "by.meta", "by.repertoire", "by.clonotype". interval(from, to): keeps rows/samples with numeric values that fits in this interval. from is inclusive, to is exclusive. Available for methods: "by.meta", "by.repertoire", "by.clonotype". Default value: 'list(CDR3.aa = exclude("partial", "out_of_frame"))'.
.match	Matching method for "include" and "exclude" options in query. Possible values: exact: matches only the exact specified string; startswith: matches all strings starting with the specified substring; substring: matches all strings containing the specified substring. Default value: 'exact'.

immunarch documentation built on Nov. 5, 2025, 7:21 p.m.