create the sequence seeds data from the given fasta sequence

create.seeds {bioseq.patterns}

R Documentation

create the sequence seeds data from the given fasta sequence

Description

collection, and then save the generated seed data into the target seed <br /> data file

Usage

create.seeds(fasta, saveto,
    minw = 8,
    maxw = 20,
    seedingCutoff = 0.95,
    scanMinW = 6,
    scanCutoff = 0.8,
    significant.sites = 4,
    debug = FALSE);

Arguments

fasta

a fasta sequence collection for make the sequence seeds, which can be a FastaFile object, a collection of the FastaSeq object, or a character vector of the raw sequence data.

saveto

a ScanFile sequence seed data file object for save the generated seed data, which is created by the open.seedFile api. [as ScanFile]

minw%

the minimum seed width in chars.

maxw%

the maximum seed width in chars.

seedingCutoff

the similarity cutoff threshold value for build the seed clusters. [as double]

scanMinW

the minimum width of the seed scan region. [as integer]

scanCutoff

the similarity score cutoff threshold value of the seed scan. [as double]

significant.sites

the minimum number of the significant sites for keep a seed. [as integer]

debug

print the debug log message of the seed scan progress?. [as boolean]

env

the R# runtime environment object. [as Environment]

Authors

seqtoolkit

Value

the input ScanFile sequence seed data file object with the generated seed data has been written into it.

clr value class

any kind

[Package bioseq.patterns version 1.0.0.0 Index]