Lookup and filter eplets unique to positive beads

get_positive_eplets() takes in results from a Luminex single antigen bead assay, and extracts only the eplets that occur exclusively on positive- but not negative beads for each sample. That is, the set of eplets on negative beads is "subtracted" from the set of eplets on positive beads.

Usage

get_positive_eplets(
  luminex_df,
  sample_col,
  alleles_col,
  assignment_col,
  eplet_df,
  pos_col = "eplets_pos"
)

Arguments

luminex_df

Data frame with Luminex assay results.

sample_col

Name of column in luminex_df containing a character vector of sample IDs.

alleles_col

Name of column in luminex_df containing a character vector of bead specificities (i.e. the HLA coated on the bead).

assignment_col

Name of column in luminex_df containing a logical vector with the bead assignment (TRUE = positive, FALSE = negative).

eplet_df

Data frame containing the Eplet Registry; from output of load_eplet_registry().

pos_col

Name of new column to contain positive-only eplets.

Value

Data frame with two columns, and one row for each eplet:

1. Character vector of sample IDs as in sample_col

2. Character vector of eplet names.

See also

lookup_eplets() is used internally to retrieve the eplets on each allele from the HLA Registry

Examples

if (FALSE) { # \dontrun{
df_eplets <- load_eplet_registry()
luminex_df <- dplyr::tribble(
  ~sampleID, ~allele, ~positive,
  "001", "A*01:01", TRUE,
  "001", "A*02:01", FALSE,
  "002", "A*01:01", TRUE
)
get_positive_eplets(luminex_df, sampleID, allele, positive, df_eplets)
} # }