tcR (version 1.3)

get.kmers: Get kmers from sequences.

Description

Get vector of kmers from the given character vector or data frame.

Usage

get.kmers(.data, .head = -1, .k = 5, .clean = T, .meat = F,
  .verbose = T, .left.shift = 0, .right.shift = 0)

Arguments

.data

Either character vector or a data.frame.

.head

Parameter for head function applied to the given data before kmer generation.

.k

Size of the kmer.

.clean

If T than remove sequences which contain '~' or '*' symbols. Useful for deleting out-of-frame aminoacid sequnces.

.meat

if TRUE than .data must be data.frame with columns CDR3.amino.acid.sequence and Read.count.

.verbose

If T than print progress.

.left.shift

Cut all .left.shift symbols from the left side for each sequence.

.right.shift

Cut all .right.shift symbols from the right side for each sequence.

Value

• Data.frame with 2 columns Kmers and Count / Rank / Proportion relatively to the .value param or a list with such data.frames if .data is a list.