simFastqqRunTimes {seqTools} | R Documentation |
simFastqqRunTimes: For given values of k and nSeq the function creates
FASTQ files with simulated data, collects k-mer data with the fastqq
function and reports the run times for the data collection.
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)
[Package
seqTools version 1.24.0
Index]