RNASeqQualityAssessment_CMD: RNASeqQualityAssessment_CMD

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

RNASeqQualityAssessment_CMD

Description

Assess the quality of '.fastq.gz' files for RNA-Seq workflow in background. This step is optional in the whole RNA-Seq workflow.
This function reports the quality assessment result in packages systemPipeR For systemPipeR, 'RNASeq_results/QA_results/Rqc/systemPipeR/fastqReport.pdf' will be created.
If you want to assess the quality of '.fastq.gz' files for the following RNA-Seq workflow in R shell, please see RNASeqQualityAssessment() function.

Usage

RNASeqQualityAssessment_CMD(RNASeqRParam, run = TRUE,
  check.s4.print = TRUE)

Arguments

RNASeqRParam	S4 object instance of experiment-related parameters
run	Default value is TRUE. If TRUE, 'Rscript/Environment_Set.R' will be created and executed. The output log will be stored in 'Rscript_out/Environment_Set.Rout'. If False, 'Rscript/Environment_Set.R' will be created without executed.
check.s4.print	Default TRUE. If TRUE, the result of checking RNASeqRParam will be reported in 'Rscript_out/Environment_Set.Rout'. If FALSE, the result of checking RNASeqRParam will not be in 'Rscript_out/Environment_Set.Rout'

Value

None

Author(s)

Kuan-Hao Chao

Examples

data(yeast)
## Not run: 
RNASeqQualityAssessment_CMD(RNASeqRParam = yeast)
## End(Not run)

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