tcR (version 2.2.4)

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

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))
# }