Filter out clonotypes from public repertoires
Filter our clonotypes with low incidence in a specific group.
pubRepFilter(.pr, .meta, .by, .min.samples = 1)
.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.Data frame with filtered clonotypes.
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)
Useful links