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Filter out clonotypes from public repertoires

Source: R/v0_public.R
pubRepFilter.Rd

[Deprecated]

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. 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
#>             <char>   <char>   <num> <num> <num> <num> <num> <num> <num>
#> 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