get.kmers: Get kmers from sequences.

In tcR: Advanced Data Analysis of Immune Receptor Repertoires

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 then 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 then 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.

tcR documentation built on July 2, 2020, 3:18 a.m.