kmer.table: Make and manage the table of the most frequent k-mers.

In tcR: Advanced Data Analysis of Immune Receptor Repertoires

Description

kmer.table - generate table with the most frequent k-mers.

get.kmer.column - get vector of k-mers from the k-mer table from the function kmer.table

Usage

kmer.table(.data, .heads = c(10, 100, 300, 1000, 3000, 10000, 30000), .k = 5, .nrow = 20,
           .clean = T, .meat = F)

get.kmer.column(.kmer.table.list, .head)

Arguments

.data	tcR data.frame or a list with tcR data.frames.
.heads	Vector of parameter for the head() function, supplied sequentialy to the get.kmers() function. -1 means all rows.
.k	Size of the kmer.
.nrow	How many most frequent k-mers include to the output table.
.clean	Parameter for the get.kmers() function.
.meat	Parameter for the get.kmers() function.
.kmer.table.list	Result from the kmer.table function if .data supplied as a list.
.head	Which columns with this head return.

Value

kmer.table - if .data is a data frame, than data frame with columns like "Kmers.X", "Count.X" where X - element from .heads. If .data is a list, than list of such data frames.

get.kmer.column - data frame with first column with kmers and other columns named as a names of data frames, from which .kmer.table.list was generated.

Examples

## Not run: 
twb.kmers <- kmer.table(twb, .heads = c(5000, 10000), .meat = T)
head(get.kmer.column(twb.kmers, 10000))

## End(Not run)

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