RNASeqRParam-class: RNASeqR
In RNASeqR: RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

An S4 class for checking and storing RNA-Seq workflow parameters of this package.

os.type: 'linux' or 'osx'. The operating system type.
python.variable: A list storing python environment. (check.answer, python.version)
python.2to3: Logical value whether 2to3 command is available on the workstation.
path.prefix: Path prefix of 'gene_data/', 'RNASeq_bin/', 'RNASeq_results/', 'Rscript/' and 'Rscript_out/' directories.
input.path.prefix: Path prefix of 'input_files/' directory,
genome.name: Variable of genome name defined in this RNA-Seq workflow (ex. genome.name.fa, genome.name.gtf).
sample.pattern: Regular expression of paired-end fastq.gz files under 'input_files/raw_fastq.gz'. Expression not includes _[1,2].fastq.gz.
independent.variable: Independent variable for the biological. experiment design of two-group RNA-Seq workflow.
case.group: Group name of the case group.
control.group: Group name of the control group.
indices.optional: Logical value whether 'indices/' is exit in 'input_files/'.
fastq.gz.type: Specify the fastq.gz file type. 'PE' represents paired-end and 'SE' represents single-end.

Kuan-Hao Chao

data(yeast)
"@"(yeast, os.type)
"@"(yeast, python.variable)
"@"(yeast, python.2to3)
"@"(yeast, path.prefix)
"@"(yeast, input.path.prefix)
"@"(yeast, genome.name)
"@"(yeast, sample.pattern)
"@"(yeast, independent.variable)
"@"(yeast, case.group)
"@"(yeast, control.group)
"@"(yeast, indices.optional)
"@"(yeast, fastq.gz.type)