RNASeqRParam-constructor: RNASeqRParam

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

RNASeqRParam

Description

Constructor function for RNASeqRParam objects

Usage

RNASeqRParam(path.prefix = NA, input.path.prefix = NA,
  genome.name = NA, sample.pattern = NA, independent.variable = NA,
  case.group = NA, control.group = NA, fastq.gz.type = NA)

Arguments

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.
fastq.gz.type	Specify the fastq.gz file type. 'PE' represents paired-end and 'SE' represents single-end.

Value

an object of class RNASeqRParam

Author(s)

kuan-hao Chao

Kuan-Hao Chao

Examples

input_files.path <- system.file("extdata/", package = "RNASeqRData")
rnaseq_result.path <- tempdir(check = TRUE)
exp <- RNASeqRParam(path.prefix          = rnaseq_result.path,
                    input.path.prefix    = input_files.path,
                    genome.name          = "Saccharomyces_cerevisiae_XV_Ensembl",
                    sample.pattern       = "SRR[0-9]*_XV",
                    independent.variable = "state",
                    case.group           = "60mins_ID20_amphotericin_B",
                    control.group        = "60mins_ID20_control",
                    fastq.gz.type        = "PE")

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