Public repertoire
pubRep(.data, .col = "aa+v", .quant = c("count", "prop"), .coding = T, .min.samples = 1, .max.samples = NA, .verbose = T)
.data | The data to be processed. Can be data.frame, data.table, or a list of these objects. Every object must have columns in the immunarch compatible format. immunarch_data_format Competent users may provide advanced data representations: DBI database connections, Apache Spark DataFrame from copy_to or a list of these objects. They are supported with the same limitations as basic objects. Note: each connection must represent a separate repertoire. |
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.col | A string that specifies the column(s) to be processed. Pass one of the following strings, separated by the plus sign: "nt" for nucleotide sequences, "aa" for amino acid sequences, "v" for V gene segments, "j" for J gene segments. E.g., pass "aa+v" to compute overlaps on CDR3 amino acid sequences paired with V gene segments, i.e., in this case a unique clonotype is a pair of CDR3 amino acid and V gene segment. |
.quant | A string that specifies the column to be processed. Pass "count" to see public clonotype sharing with the number of clones, pass "prop" to see proportions. |
.coding | Logical. If TRUE then preprocess the data to filter out non-coding sequences. |
.min.samples | Integer. A minimal number of samples a clonotype must have to be included in the public repertoire table. |
.max.samples | Integer. A maxminal number of samples a clonotype must have to be included in the public repertoire table. Pass NA (by default) to have the maximal amoount of samples. |
.verbose | Logical. If TRUE then output the progress. |