Summarize a meta-clonotype's composition

Reports the V/J gene usage, CDR3 length distribution, and subject representation within a meta-clonotype neighborhood.

Usage

summarize_meta_clonotype(tcr_df, center_idx, neighbor_indices)

Arguments

tcr_df

Data.frame with TCR columns.

center_idx

Integer. Row index of the center TCR.

neighbor_indices

Integer vector. Row indices of neighbors.

Value

A named list:

center

Named list of center TCR fields.

n_members

Number of members.

va_usage

Named integer vector of V-alpha gene counts.

vb_usage

Named integer vector of V-beta gene counts.

cdr3a_lengths

Integer vector of CDR3-alpha lengths.

cdr3b_lengths

Integer vector of CDR3-beta lengths.

See also

find_meta_clonotypes

Examples

if (FALSE) { # \dontrun{
meta <- find_meta_clonotypes(tcr_df, "mouse", radius = 30,
                              subject_col = "subject")
if (nrow(meta) > 0) {
    indices <- as.integer(strsplit(meta$neighbor_indices[1], ",")[[1]])
    summary <- summarize_meta_clonotype(
        tcr_df, meta$center_index[1], indices)
    summary$n_members
    summary$va_usage
}
} # }