simFastqqRunTimes: simFastqqRunTimes: For given values of k and nSeq the...

In wokai/seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

Description

For each combination of the parameters k and nSeq, the function writes one FASTQ file and collects the data. The FASTQ files are equally structured: Each read contains 17 randomly selected DNA 6-mers. Therefore the read-length is always 102.

Usage

simFastqqRunTimes(k, nSeq, filedir=".")

Arguments

k	numeric. k-mer sizes which are passed to fastqq. Default value is 2:15.

nSeq	numeric. Number of simulated reads in FASTQ-file. Default value is (100, 1000, ..., 10000000).

filedir

character. The output can be placed in a separate directory. When not existant, the function tries to create 'filedir'. The function throws an error when writing is not permitted in the given directory (Could not open file ...).

Details

The FASTQ files contain the parameter settings inside their filename. The files are created with 'writeSimFastq'.

Value

data.frame. The data frame has four columns: id, k, nSeq and runtime.

Author(s)

Wolfgang Kaisers

Examples

## Not run: 
res <- simFastqqRunTimes(k=2:9, nSeq=100000)
plot(runtime~k,res,type="b")

## End(Not run)

wokai/seqTools documentation built on May 4, 2019, 9:46 a.m.