Calculate the k-mer statistics of immune repertoires
getKmers(.data, .k, .col = c("aa", "nt"), .coding = TRUE)
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.
Integer. Length of k-mers.
Character. Which column to use, pass "aa" (by default) for CDR3 amino acid sequence, pass "nt" for CDR3 nucleotide sequences.
Logical. If TRUE (by default) then removes all non-coding sequences from input data first.
Data frame with two columns (k-mers and their counts).