R: Filter out clonotypes from public repertoires

pubRepFilter {immunarch} | 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. Filter 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)

[Package immunarch version 0.6.5 Index]