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

Description Usage Arguments Details Value Author(s) Examples

View source: R/simFunctions.r

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 k-mers of size 6. Therefore the read-length is always 102.

Usage

1
simFastqqRunTimes(k,nSeq,filedir=".")

Arguments

k

numeric. Length of k-mer. 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

1
simFastqqRunTimes(k=5,nSeq=10)

seqTools documentation built on May 31, 2017, 1:59 a.m.