compareQA: Compares quality before and after filtering fastq files....

In nixstix/RNASeqAnalysis: Analysis of RNA-Seq data: QC filtering, expression analysis, differential expression pipeline

Description

Compares quality before and after filtering fastq files. Provides a graphic of the change in quality of fastq files, before and after running the filterBadSeqs function.

Usage

compareQA(dataFile, prefiltData, postfiltData)

Arguments

dataFile	An R data frame with the data to be processed. The R object is a standard format, and must contain the following headings: File, PE, Sample, Replicate, FilteredFile. More information about the file is available at datafileTemplate. The checkDataFile function should be run on the file before use.
prefiltData	A FastqQA object resulting from runQA. The object contains QA data on fastq files before the filtering procedure (filterBadSeqs).
postfiltData	A FastqQA object resulting from runQA. The object contains QA data on fastq files after the filtering procedure (filterBadSeqs).

Value

a datafrome containing densities and quality scores for each fastq file (both before and after filtering). It also outputs a graph which shows comparisons of quality before and after filtering.

nixstix/RNASeqAnalysis documentation built on May 23, 2019, 7:06 p.m.