pubRepFilter function

Filter out clonotypes from public repertoires

Filter out clonotypes from public repertoires

Filter our clonotypes with low incidence in a specific group.

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.

Returns

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)
  • Maintainer: Vadim I. Nazarov
  • License: Apache License (== 2.0)
  • Last published: 2024-03-18