Immune repertoire spectratyping

spectratype(.data, .quant = c("id", "count"), .col = "nt")



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.


Select the column with clonal counts to evaluate. Pass "id" to count every clonotype once. Pass "count" to take into the account number of clones per clonotype.


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" for spectratyping 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. Clonal counts of equal clonotypes will be summed up.


Data frame with distributions of clonotypes per CDR3 length.


# Load the data data(immdata) sp <- spectratype(immdata$data[[1]], .col="aa+v") vis(sp)