Kmer analysis of repertoires.
getKmers(.data, .k, .col = c("aa", "nt"), .coding = 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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.k | Integer. Length of kmers. |
.col | Character. Which column to use, pass "aa" (by default) for CDR3 amino acid sequence, pass "nt" for CDR3 nucleotide sequences. |
.coding | Logical. If TRUE (by default) then remove all non-coding sequences from input data first. |