In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

knitr::opts_chunk$set(echo = TRUE,warning=FALSE, message=FALSE,out.width="70%")
## This report requires summary files form mothur
debug <- FALSE

Started on r format(Sys.time(), "%Y-%m-%d %H:%M:%S")

Data pre-processing {.tabset}

Summary of the raw reads

RDSplot <- plotFromMothurSumm(finalListOfSummaryTables["RawDataSummary"]$RawDataSummary)
plot(RDSplot)

Summary of the deduplicated reads

DDplot <- plotFromMothurSumm(finalListOfSummaryTables["DeduppedSummary"]$DeduppedSummary)
plot(DDplot)

Summary of the reads filtered by length and homopolymers

LHplot <- plotFromMothurSumm(finalListOfSummaryTables["LenAndHomopSummary"]$LenAndHomopSummary)
plot(LHplot)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.