pubRepFilter: Filter out clonotypes from public repertoires

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

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)

immunomind/immunarch documentation built on March 20, 2024, 12:01 p.m.