RNASeqQualityAssessment: RNASeqQualityAssessment

View source: R/cmd_batch_rnaseq_quality_assessment.R

RNASeqQualityAssessmentR Documentation

RNASeqQualityAssessment

Description

Assess the quality of '.fastq.gz' files for RNA-Seq workflow in R shell. 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 background, please see RNASeqQualityAssessment_CMD() function.

Usage

RNASeqQualityAssessment(RNASeqRParam, which.trigger = "OUTSIDE",
  INSIDE.path.prefix = NA, check.s4.print = TRUE)

Arguments

RNASeqRParam

S4 object instance of experiment-related parameters

which.trigger

Default value is OUTSIDE. User should not change this value.

INSIDE.path.prefix

Default value is NA. User should not change this value.

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(RNASeqRParam = yeast)
## End(Not run)

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