RNASeqQualityAssessment: RNASeqQualityAssessment

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

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)

Kuanhao-Chao/RNASeqR documentation built on May 12, 2022, 8:15 a.m.