RNASeqRParam-class: RNASeqR

In HowardChao/RNASeqWorkflow: RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

RNASeqR

Description

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

Slots

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.

Author(s)

Kuan-Hao Chao

Examples

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)

HowardChao/RNASeqWorkflow documentation built on May 9, 2022, 10:49 a.m.