kallistoAssembleQC: Collect kallisto and fastqc information.

In RGLab/RNASeqPipelineR: Construct Standardized pipelines for processing RNASeq data

Description

Assemble kallisto and fastqc QC information and potentially combine with annotation data. Write 'kallisto_Pheno.csv' to OUTPUT directory.

Usage

kallistoAssembleQC(paired = TRUE, doAnnotation = TRUE,
  phenoMatchLabel = "Sample")

Arguments

paired	if TRUE then paired end data else single read data
doAnnotation	if TRUE then add annotation data to qc info. The annotation file must be the sole .csv file in the RAW_ANNOTATIONS directory.
phenoMatchLabel	column name that contains the fastq file names without the paired suffix label in the annotation data. Used to match information between the phenotype annotation file, kallisto QC, and FASTQC information. Defaults to 'Sample'. Not used if doAnnotation is FALSE.

RGLab/RNASeqPipelineR documentation built on Jan. 19, 2020, 12:31 a.m.