Now open the R markdown script systemPipeVARseq.Rmdin your R IDE (e.g. vim-r or RStudio) and
run the workflow as outlined below.
Load packages and sample data
The systemPipeR package needs to be loaded to perform the analysis steps shown in
this report (Girke , 2015).
library(systemPipeR)
Load workflow environment with sample data into your current working directory. The sample data are described here.
library(systemPipeRdata)
genWorkenvir(workflow="varseq")
setwd("varseq")
download.file("https://raw.githubusercontent.com/tgirke/GEN242/master/vignettes/13_VARseqWorkflow/systemPipeVARseq.Rmd", "systemPipeVARseq.Rmd")
In the workflow environments generated by genWorkenvir all data inputs are stored in
a data/ directory and all analysis results will be written to a separate
results/ directory, while the systemPipeVARseq.Rmd script and the targets file are expected to be located in
the parent directory. The R session is expected to run from this parent
directory. Additional parameter files are stored under param/.
To work with real data, users want to organize their own data similarly
and substitute all test data for their own data. To rerun an established
workflow on new data, the initial targets file along with the corresponding
FASTQ files are usually the only inputs the user needs to provide.
If applicable users can load custom functions not provided by systemPipeR. Skip
this step if this is not the case.
source("systemPipeChIPseq_Fct.R")
Experiment definition provided by targets file
The targets file defines all FASTQ files and sample comparisons of the analysis workflow.
targetspath <- system.file("extdata", "targetsPE.txt", package="systemPipeR")
targets <- read.delim(targetspath, comment.char = "#")
targets[,-c(5,6)]
## FileName1 FileName2 SampleName Factor Date
## 1 ./data/SRR446027_1.fastq ./data/SRR446027_2.fastq M1A M1 23-Mar-2012
## 2 ./data/SRR446028_1.fastq ./data/SRR446028_2.fastq M1B M1 23-Mar-2012
## 3 ./data/SRR446029_1.fastq ./data/SRR446029_2.fastq A1A A1 23-Mar-2012
## 4 ./data/SRR446030_1.fastq ./data/SRR446030_2.fastq A1B A1 23-Mar-2012
## 5 ./data/SRR446031_1.fastq ./data/SRR446031_2.fastq V1A V1 23-Mar-2012
## 6 ./data/SRR446032_1.fastq ./data/SRR446032_2.fastq V1B V1 23-Mar-2012
## 7 ./data/SRR446033_1.fastq ./data/SRR446033_2.fastq M6A M6 23-Mar-2012
## 8 ./data/SRR446034_1.fastq ./data/SRR446034_2.fastq M6B M6 23-Mar-2012
## 9 ./data/SRR446035_1.fastq ./data/SRR446035_2.fastq A6A A6 23-Mar-2012
## 10 ./data/SRR446036_1.fastq ./data/SRR446036_2.fastq A6B A6 23-Mar-2012
## 11 ./data/SRR446037_1.fastq ./data/SRR446037_2.fastq V6A V6 23-Mar-2012
## 12 ./data/SRR446038_1.fastq ./data/SRR446038_2.fastq V6B V6 23-Mar-2012
## 13 ./data/SRR446039_1.fastq ./data/SRR446039_2.fastq M12A M12 23-Mar-2012
## 14 ./data/SRR446040_1.fastq ./data/SRR446040_2.fastq M12B M12 23-Mar-2012
## 15 ./data/SRR446041_1.fastq ./data/SRR446041_2.fastq A12A A12 23-Mar-2012
## 16 ./data/SRR446042_1.fastq ./data/SRR446042_2.fastq A12B A12 23-Mar-2012
## 17 ./data/SRR446043_1.fastq ./data/SRR446043_2.fastq V12A V12 23-Mar-2012
## 18 ./data/SRR446044_1.fastq ./data/SRR446044_2.fastq V12B V12 23-Mar-2012