collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files.

Description

Objects of class Fastqq are created by reading data from FASTQ-files using the function fastqq. The fastqq function calls Sys.time() before and after execution of the core collecting routine. collectDur returns the number of seconds between these two times (as numeric value). collectTime returns the two timestamps inside a list.

Usage

collectDur(object)
collectTime(object)

Arguments

Value

collectTime returns numeric. collectTime returns list.

Author(s)

Wolfgang Kaisers

See Also

fastqq

Examples

basedir <- system.file("extdata", package="seqTools")
setwd(basedir)
fq<-fastqq(c("g4_l101_n100.fq.gz", "g5_l101_n100.fq.gz"), k=4,
            probeLabel=c("g4", "g5"))

collectTime(fq)
collectDur(fq)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(seqTools)
Loading required package: zlibbioc
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/seqTools/collectDur.Rd_%03d_medium.png", width=480, height=480)
> ### Name: collectDur
> ### Title: collectDur: Returning elapsed time (in seconds) for collection
> ###   of data from FASTQ files.
> ### Aliases: collectTime collectTime-methods collectTime,Fastqq-method
> ###   collectDur collectDur-methods collectDur,Fastqq-method
> ### Keywords: collectDur
> 
> ### ** Examples
> 
> basedir <- system.file("extdata", package="seqTools")
> setwd(basedir)
> fq<-fastqq(c("g4_l101_n100.fq.gz", "g5_l101_n100.fq.gz"), k=4,
+             probeLabel=c("g4", "g5"))
[fastqq] File ( 1/2) 'g4_l101_n100.fq.gz'	done.
[fastqq] File ( 2/2) 'g5_l101_n100.fq.gz'	done.
> 
> collectTime(fq)
$start
[1] "2016-07-07 06:42:22 JST"

$end
[1] "2016-07-07 06:42:22 JST"

> collectDur(fq)
[1] 0.001020908
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>