repFilter: Main function for data filtering

In immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

Main function for data filtering

Description

Main function for data filtering

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'.

Examples

data(immdata)

# Select samples with status "MS"
repFilter(immdata, "by.meta", list(Status = include("MS")))

# Select samples without status "MS"
repFilter(immdata, "by.meta", list(Status = exclude("MS")))

# Select samples from lanes "A" and "B" with age > 15
repFilter(immdata, "by.meta", list(Lane = include("A", "B"), Age = morethan(15)))

# Select samples that are not from lanes "A" and "B"
repFilter(immdata, "by.meta", list(Lane = exclude("A", "B")))

# Select samples with a number of clonotypes from 1000 to 5000
repFilter(immdata, "by.repertoire", list(n_clonotypes = interval(1000, 5000)))

# Select clonotypes in all samples with alpha chains
repFilter(immdata, "by.clonotype",
  list(V.name = include("AV"), J.name = include("AJ")),
  .match = "substring"
)

immunarch documentation built on Dec. 28, 2022, 2:59 a.m.