pubRepFilter: Filter out clonotypes from public repertoires
In immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

pubRepFilter

R Documentation

Filter out clonotypes from public repertoires

Description

Filter our clonotypes with low incidence in a specific group.

Usage

pubRepFilter(.pr, .meta, .by, .min.samples = 1)

Arguments

`.pr`	Public repertoires, an output from pubRep.
`.meta`	Metadata file.
`.by`	Named character vector. Names of the group to filter by.
`.min.samples`	Integer. Filters out clonotypes with the number of samples below than this number.

Value

Data frame with filtered clonotypes.

Examples

data(immdata)
immdata$data <- lapply(immdata$data, head, 2000)
pr <- pubRep(immdata$data, .verbose = FALSE)
pr1 <- pubRepFilter(pr, immdata$meta, .by = c(Status = "MS"))
head(pr1)

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