Last data update: 2014.03.03
R: Class '"SYSargs"'
SYSargs-class R Documentation
Class "SYSargs"
Description
S4 class container for storing parameters of command-line- or R-based software.
SYSargs instances are constructed by the systemArgs function
from two simple tablular files: a targets file and a param file.
The latter is optional for workflow steps lacking command-line software.
Typically, a SYSargs instance stores all sample-level inputs as well as
the paths to the corresponding outputs generated by command-line- or R-based
software generating sample-level output files. Each sample level input/outfile
operation uses its own SYSargs instance. The outpaths of SYSargs
usually define the sample inputs for the next SYSargs instance. This
connectivity is achieved by writing the outpaths with the
writeTargetsout function to a new targets file that serves as input to
the next systemArgs call. By chaining several SYSargs steps
together one can construct complex workflows involving many sample-level
input/output file operations with any combinaton of command-line or R-based
software.
Objects from the Class
Objects can be created by calls of the form new("SYSargs", ...).
Slots
targetsin:Object of class "data.frame" storing tabular data from targets input file
targetsout:Object of class "data.frame" storing tabular data from targets output file
targetsheader:Object of class "character" storing header/comment lines of targets file
modules:Object of class "character" storing software versions from module system
software:Object of class "character" name of executable of command-line software
cores:Object of class "numeric" number of CPU cores to use
other:Object of class "character" additional arguments
reference:Object of class "character" path to reference genome file
results:Object of class "character" path to results directory
infile1:Object of class "character" paths to first FASTQ file
infile2:Object of class "character" paths to second FASTQ file if data is PE
outfile1:Object of class "character" paths to output files generated by command-line software
sysargs:Object of class "character" full commands used to execute external software
outpaths:Object of class "character" paths to final outputs including postprocessing by Rsamtools
Methods
SampleName signature(x = "SYSargs"): extracts sample names
[ signature(x = "SYSargs"): subsetting of class with bracket operator
coerce signature(from = "list", to = "SYSargs"): as(list, "SYSargs")
cores signature(x = "SYSargs"): extracts data from cores slot
infile1 signature(x = "SYSargs"): extracts data from infile1 slot
infile2 signature(x = "SYSargs"): extracts data from infile2 slot
modules signature(x = "SYSargs"): extracts data from modules slot
names signature(x = "SYSargs"): extracts slot names
length signature(x = "SYSargs"): extracts number of samples
other signature(x = "SYSargs"): extracts data from other slot
outfile1 signature(x = "SYSargs"): extracts data from outfile1 slot
outpaths signature(x = "SYSargs"): extracts data from outpath slot
reference signature(x = "SYSargs"): extracts data from reference slot
results signature(x = "SYSargs"): extracts data from results slot
show signature(object = "SYSargs"): summary view of SYSargs objects
software signature(x = "SYSargs"): extracts data from software slot
targetsheader signature(x = "SYSargs"): extracts data from targetsheader slot
targetsin signature(x = "SYSargs"): extracts data from targetsin slot
targetsout signature(x = "SYSargs"): extracts data from targetsout slot
Author(s)
Thomas Girke
See Also
systemArgs and runCommandline
Examples
showClass("SYSargs")
## Construct SYSargs object from param and targets files
param <- system.file("extdata", "tophat.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args <- systemArgs(sysma=param, mytargets=targets)
args
names(args); targetsin(args); targetsout(args); targetsheader(args);
software(args); modules(args); cores(args); outpaths(args)
sysargs(args); other(args); reference(args); results(args); infile1(args)
infile2(args); outfile1(args); SampleName(args)
## Return sample comparisons
readComp(args, format = "vector", delim = "-")
## The subsetting operator '[' allows to select specific samples
args[1:4]
## Not run:
## Execute SYSargs on single machine
runCommandline(args=args)
## Execute SYSargs on multiple machines
qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(args), memory="mem=10gb", time="walltime=20:00:00")
qsubRun(appfct="runCommandline(args=args)", appargs=args, qsubargs=qsubargs, Nqsubs=1, submitdir="results", package="systemPipeR")
## Write outpaths to new targets file for next SYSargs step
writeTargetsout(x=args, file="default")
## End(Not run)
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(systemPipeR)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/systemPipeR/SYSargs-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: SYSargs-class
> ### Title: Class '"SYSargs"'
> ### Aliases: SYSargs-class [,SYSargs,ANY,ANY,ANY-method
> ### coerce,list,SYSargs-method cores,SYSargs-method
> ### infile1,SYSargs-method infile2,SYSargs-method modules,SYSargs-method
> ### names,SYSargs-method length,SYSargs-method other,SYSargs-method
> ### results,SYSargs-method outfile1,SYSargs-method
> ### outpaths,SYSargs-method reference,SYSargs-method show,SYSargs-method
> ### software,SYSargs-method sysargs,SYSargs-method
> ### SampleName,SYSargs-method targetsheader,SYSargs-method
> ### targetsin,SYSargs-method targetsout,SYSargs-method
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("SYSargs")
Class "SYSargs" [package "systemPipeR"]
Slots:
Name: targetsin targetsout targetsheader modules software
Class: data.frame data.frame character character character
Name: cores other reference results infile1
Class: numeric character character character character
Name: infile2 outfile1 sysargs outpaths
Class: character character character character
> ## Construct SYSargs object from param and targets files
> param <- system.file("extdata", "tophat.param", package="systemPipeR")
> targets <- system.file("extdata", "targets.txt", package="systemPipeR")
> args <- systemArgs(sysma=param, mytargets=targets)
There were 18 warnings (use warnings() to see them)
> args
An instance of 'SYSargs' for running 'tophat' on 18 samples
> names(args); targetsin(args); targetsout(args); targetsheader(args);
[1] "targetsin" "targetsout" "targetsheader" "modules"
[5] "software" "cores" "other" "reference"
[9] "results" "infile1" "infile2" "outfile1"
[13] "sysargs" "outpaths"
FileName SampleName Factor SampleLong Experiment Date
1 ./data/SRR446027_1.fastq M1A M1 Mock.1h.A 1 23-Mar-2012
2 ./data/SRR446028_1.fastq M1B M1 Mock.1h.B 1 23-Mar-2012
3 ./data/SRR446029_1.fastq A1A A1 Avr.1h.A 1 23-Mar-2012
4 ./data/SRR446030_1.fastq A1B A1 Avr.1h.B 1 23-Mar-2012
5 ./data/SRR446031_1.fastq V1A V1 Vir.1h.A 1 23-Mar-2012
6 ./data/SRR446032_1.fastq V1B V1 Vir.1h.B 1 23-Mar-2012
7 ./data/SRR446033_1.fastq M6A M6 Mock.6h.A 1 23-Mar-2012
8 ./data/SRR446034_1.fastq M6B M6 Mock.6h.B 1 23-Mar-2012
9 ./data/SRR446035_1.fastq A6A A6 Avr.6h.A 1 23-Mar-2012
10 ./data/SRR446036_1.fastq A6B A6 Avr.6h.B 1 23-Mar-2012
11 ./data/SRR446037_1.fastq V6A V6 Vir.6h.A 1 23-Mar-2012
12 ./data/SRR446038_1.fastq V6B V6 Vir.6h.B 1 23-Mar-2012
13 ./data/SRR446039_1.fastq M12A M12 Mock.12h.A 1 23-Mar-2012
14 ./data/SRR446040_1.fastq M12B M12 Mock.12h.B 1 23-Mar-2012
15 ./data/SRR446041_1.fastq A12A A12 Avr.12h.A 1 23-Mar-2012
16 ./data/SRR446042_1.fastq A12B A12 Avr.12h.B 1 23-Mar-2012
17 ./data/SRR446043_1.fastq V12A V12 Vir.12h.A 1 23-Mar-2012
18 ./data/SRR446044_1.fastq V12B V12 Vir.12h.B 1 23-Mar-2012
FileName
1 /home/ddbj/DataUpdator-rgm3/target/results/SRR446027_1.fastq.tophat/accepted_hits.bam
2 /home/ddbj/DataUpdator-rgm3/target/results/SRR446028_1.fastq.tophat/accepted_hits.bam
3 /home/ddbj/DataUpdator-rgm3/target/results/SRR446029_1.fastq.tophat/accepted_hits.bam
4 /home/ddbj/DataUpdator-rgm3/target/results/SRR446030_1.fastq.tophat/accepted_hits.bam
5 /home/ddbj/DataUpdator-rgm3/target/results/SRR446031_1.fastq.tophat/accepted_hits.bam
6 /home/ddbj/DataUpdator-rgm3/target/results/SRR446032_1.fastq.tophat/accepted_hits.bam
7 /home/ddbj/DataUpdator-rgm3/target/results/SRR446033_1.fastq.tophat/accepted_hits.bam
8 /home/ddbj/DataUpdator-rgm3/target/results/SRR446034_1.fastq.tophat/accepted_hits.bam
9 /home/ddbj/DataUpdator-rgm3/target/results/SRR446035_1.fastq.tophat/accepted_hits.bam
10 /home/ddbj/DataUpdator-rgm3/target/results/SRR446036_1.fastq.tophat/accepted_hits.bam
11 /home/ddbj/DataUpdator-rgm3/target/results/SRR446037_1.fastq.tophat/accepted_hits.bam
12 /home/ddbj/DataUpdator-rgm3/target/results/SRR446038_1.fastq.tophat/accepted_hits.bam
13 /home/ddbj/DataUpdator-rgm3/target/results/SRR446039_1.fastq.tophat/accepted_hits.bam
14 /home/ddbj/DataUpdator-rgm3/target/results/SRR446040_1.fastq.tophat/accepted_hits.bam
15 /home/ddbj/DataUpdator-rgm3/target/results/SRR446041_1.fastq.tophat/accepted_hits.bam
16 /home/ddbj/DataUpdator-rgm3/target/results/SRR446042_1.fastq.tophat/accepted_hits.bam
17 /home/ddbj/DataUpdator-rgm3/target/results/SRR446043_1.fastq.tophat/accepted_hits.bam
18 /home/ddbj/DataUpdator-rgm3/target/results/SRR446044_1.fastq.tophat/accepted_hits.bam
SampleName Factor SampleLong Experiment Date
1 M1A M1 Mock.1h.A 1 23-Mar-2012
2 M1B M1 Mock.1h.B 1 23-Mar-2012
3 A1A A1 Avr.1h.A 1 23-Mar-2012
4 A1B A1 Avr.1h.B 1 23-Mar-2012
5 V1A V1 Vir.1h.A 1 23-Mar-2012
6 V1B V1 Vir.1h.B 1 23-Mar-2012
7 M6A M6 Mock.6h.A 1 23-Mar-2012
8 M6B M6 Mock.6h.B 1 23-Mar-2012
9 A6A A6 Avr.6h.A 1 23-Mar-2012
10 A6B A6 Avr.6h.B 1 23-Mar-2012
11 V6A V6 Vir.6h.A 1 23-Mar-2012
12 V6B V6 Vir.6h.B 1 23-Mar-2012
13 M12A M12 Mock.12h.A 1 23-Mar-2012
14 M12B M12 Mock.12h.B 1 23-Mar-2012
15 A12A A12 Avr.12h.A 1 23-Mar-2012
16 A12B A12 Avr.12h.B 1 23-Mar-2012
17 V12A V12 Vir.12h.A 1 23-Mar-2012
18 V12B V12 Vir.12h.B 1 23-Mar-2012
[1] "# Project ID: Arabidopsis - Pseudomonas alternative splicing study (SRA: SRP010938; PMID: 24098335)"
[2] "# The following line(s) allow to specify the contrasts needed for comparative analyses, such as DEG identification. All possible comparisons can be specified with 'CMPset: ALL'."
[3] "# <CMP> CMPset1: M1-A1, M1-V1, A1-V1, M6-A6, M6-V6, A6-V6, M12-A12, M12-V12, A12-V12"
[4] "# <CMP> CMPset2: ALL"
> software(args); modules(args); cores(args); outpaths(args)
[1] "tophat"
[1] "bowtie2/2.2.5" "tophat/2.0.14"
[1] 4
M1A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446027_1.fastq.tophat/accepted_hits.bam"
M1B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446028_1.fastq.tophat/accepted_hits.bam"
A1A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446029_1.fastq.tophat/accepted_hits.bam"
A1B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446030_1.fastq.tophat/accepted_hits.bam"
V1A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446031_1.fastq.tophat/accepted_hits.bam"
V1B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446032_1.fastq.tophat/accepted_hits.bam"
M6A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446033_1.fastq.tophat/accepted_hits.bam"
M6B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446034_1.fastq.tophat/accepted_hits.bam"
A6A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446035_1.fastq.tophat/accepted_hits.bam"
A6B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446036_1.fastq.tophat/accepted_hits.bam"
V6A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446037_1.fastq.tophat/accepted_hits.bam"
V6B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446038_1.fastq.tophat/accepted_hits.bam"
M12A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446039_1.fastq.tophat/accepted_hits.bam"
M12B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446040_1.fastq.tophat/accepted_hits.bam"
A12A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446041_1.fastq.tophat/accepted_hits.bam"
A12B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446042_1.fastq.tophat/accepted_hits.bam"
V12A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446043_1.fastq.tophat/accepted_hits.bam"
V12B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446044_1.fastq.tophat/accepted_hits.bam"
> sysargs(args); other(args); reference(args); results(args); infile1(args)
M1A
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446027_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446027_1.fastq "
M1B
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446028_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446028_1.fastq "
A1A
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446029_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446029_1.fastq "
A1B
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446030_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446030_1.fastq "
V1A
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446031_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446031_1.fastq "
V1B
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446032_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446032_1.fastq "
M6A
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446033_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446033_1.fastq "
M6B
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446034_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446034_1.fastq "
A6A
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446035_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446035_1.fastq "
A6B
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446036_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446036_1.fastq "
V6A
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446037_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446037_1.fastq "
V6B
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446038_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446038_1.fastq "
M12A
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446039_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446039_1.fastq "
M12B
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446040_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446040_1.fastq "
A12A
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446041_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446041_1.fastq "
A12B
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446042_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446042_1.fastq "
V12A
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446043_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446043_1.fastq "
V12B
"tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/ddbj/DataUpdator-rgm3/target/results/SRR446044_1.fastq.tophat /home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta ./data/SRR446044_1.fastq "
[1] "-g 1 --segment-length 25 -i 30 -I 3000"
[1] "/home/ddbj/DataUpdator-rgm3/target/data/tair10.fasta"
[1] "/home/ddbj/DataUpdator-rgm3/target/results/"
M1A M1B
"./data/SRR446027_1.fastq" "./data/SRR446028_1.fastq"
A1A A1B
"./data/SRR446029_1.fastq" "./data/SRR446030_1.fastq"
V1A V1B
"./data/SRR446031_1.fastq" "./data/SRR446032_1.fastq"
M6A M6B
"./data/SRR446033_1.fastq" "./data/SRR446034_1.fastq"
A6A A6B
"./data/SRR446035_1.fastq" "./data/SRR446036_1.fastq"
V6A V6B
"./data/SRR446037_1.fastq" "./data/SRR446038_1.fastq"
M12A M12B
"./data/SRR446039_1.fastq" "./data/SRR446040_1.fastq"
A12A A12B
"./data/SRR446041_1.fastq" "./data/SRR446042_1.fastq"
V12A V12B
"./data/SRR446043_1.fastq" "./data/SRR446044_1.fastq"
> infile2(args); outfile1(args); SampleName(args)
M1A M1B A1A A1B V1A V1B M6A M6B A6A A6B V6A V6B M12A M12B A12A A12B
"" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
V12A V12B
"" ""
M1A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446027_1.fastq.tophat"
M1B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446028_1.fastq.tophat"
A1A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446029_1.fastq.tophat"
A1B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446030_1.fastq.tophat"
V1A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446031_1.fastq.tophat"
V1B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446032_1.fastq.tophat"
M6A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446033_1.fastq.tophat"
M6B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446034_1.fastq.tophat"
A6A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446035_1.fastq.tophat"
A6B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446036_1.fastq.tophat"
V6A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446037_1.fastq.tophat"
V6B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446038_1.fastq.tophat"
M12A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446039_1.fastq.tophat"
M12B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446040_1.fastq.tophat"
A12A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446041_1.fastq.tophat"
A12B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446042_1.fastq.tophat"
V12A
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446043_1.fastq.tophat"
V12B
"/home/ddbj/DataUpdator-rgm3/target/results/SRR446044_1.fastq.tophat"
[1] "M1A" "M1B" "A1A" "A1B" "V1A" "V1B" "M6A" "M6B" "A6A" "A6B"
[11] "V6A" "V6B" "M12A" "M12B" "A12A" "A12B" "V12A" "V12B"
>
> ## Return sample comparisons
> readComp(args, format = "vector", delim = "-")
$CMPset1
[1] "M1-A1" "M1-V1" "A1-V1" "M6-A6" "M6-V6" "A6-V6" "M12-A12"
[8] "M12-V12" "A12-V12"
$CMPset2
[1] "M1-A1" "M1-V1" "M1-M6" "M1-A6" "M1-V6" "M1-M12" "M1-A12"
[8] "M1-V12" "A1-V1" "A1-M6" "A1-A6" "A1-V6" "A1-M12" "A1-A12"
[15] "A1-V12" "V1-M6" "V1-A6" "V1-V6" "V1-M12" "V1-A12" "V1-V12"
[22] "M6-A6" "M6-V6" "M6-M12" "M6-A12" "M6-V12" "A6-V6" "A6-M12"
[29] "A6-A12" "A6-V12" "V6-M12" "V6-A12" "V6-V12" "M12-A12" "M12-V12"
[36] "A12-V12"
>
> ## The subsetting operator '[' allows to select specific samples
> args[1:4]
An instance of 'SYSargs' for running 'tophat' on 4 samples
>
> ## Not run:
> ##D ## Execute SYSargs on single machine
> ##D runCommandline(args=args)
> ##D
> ##D ## Execute SYSargs on multiple machines
> ##D qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(args), memory="mem=10gb", time="walltime=20:00:00")
> ##D qsubRun(appfct="runCommandline(args=args)", appargs=args, qsubargs=qsubargs, Nqsubs=1, submitdir="results", package="systemPipeR")
> ##D
> ##D ## Write outpaths to new targets file for next SYSargs step
> ##D writeTargetsout(x=args, file="default")
> ## End(Not run)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.