Filter out clonotypes from public repertoires

Source: R/public.R

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.

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)
#>            CDR3.aa   V.name Samples MS1 MS2 MS3 MS4 MS5 MS6
#> 1:     CASSLEETQYF  TRBV5-1       4  NA  NA   1   1   1   1
#> 2:     CASSFQETQYF  TRBV5-1       3  NA   1  NA   1  NA   1
#> 3:     CASSLGETQYF TRBV12-4       3   1  NA  NA  NA   1   1
#> 4: CASSDSSGSTDTQYF  TRBV6-4       2  NA  NA   1  NA  NA   2
#> 5:  CSARLAGGQETQYF TRBV20-1       2  NA  NA   1  NA  NA   1
#> 6: CASSDSAGGTDTQYF  TRBV6-4       1  NA  NA   1  NA  NA  NA