pubRepApply: Apply transformations to public repertoires

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

Apply transformations to public repertoires

Description

Work In Progress

Usage

pubRepApply(.pr1, .pr2, .fun = function(x) log10(x[1])/log10(x[2]))

Arguments

.pr1	First public repertoire.
.pr2	Second public repertoire.
.fun	A function to apply to pairs of frequencies of same clonotypes from "pr1" and "pr2". By default - log(X) / log(Y) where X,Y - frequencies of the same clonotype, found in both public repertoires.

Value

Work in progress.

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"))
pr2 <- pubRepFilter(pr, immdata$meta, .by = c(Status = "C"))
prapp <- pubRepApply(pr1, pr2)
head(prapp)

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