An Introduction to sangeranalyseR

In sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

BiocStyle::markdown()
knitr::opts_chunk$set(tidy = FALSE,
                      warning = FALSE,
                      message = FALSE)

library(sangeranalyseR)

Introduction

sangeranalyseR is an R package for analysing Sanger sequencing reads, especially those from ABIF platform, in pure R environment. There are three levels in sangeranalyseR which are 'SangerRead', 'SangerContig' and 'SangerAlignment'. Users can choose which level to start the analysis. In this documentation, we intoduce analysis workflow step by step in these three levels with examples.

SangerRead

'SangerRead' extends from 'sangerseq' class and stores 'abif' class in sangerseqR as well as essential information including quality trimming and chromatogram parameters. It corresponds to a single ABIF file in Sanger sequencing.

2.1      Create **SangerRead** Instance

First step is to create a 'SangerRead' instance. Here, we find the the abosulte file path and assign it to A_chloroticaFdReadFN.

inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")

A_chloroticaFdReadFN <- file.path(inputFilesPath, 
                          "Allolobophora_chlorotica",
                          "RBNII",
                          "Achl_RBNII396-13_1_F.ab1")

Now we can create a 'SangerRead' instance by running SangerRead constructor function.

singleRead <- SangerRead(readFeature   = "Forward Read",
                         readFileName  = A_chloroticaFdReadFN)

2.2      Visualize Trimmed Read

Second step is to visualize the trimmed read. qualityBasePlot triggers a plot_ly interactive plot for users to check the result of the trimmed read.

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2.3      Update Trimming Parameters

Third step is to change trimming parameters. SangerRead constructor function uses default trimming parameters. If users are not satisfied with the trimming result, they can run updateQualityParam function to change the trimming parameters inside the 'SangerRead' instance.

updateQualityParam(singleRead,
                   TrimmingMethod         = "M1",
                   M1TrimmingCutoff       = 0.0003,
                   M2CutoffQualityScore   = NULL,
                   M2SlidingWindowSize    = NULL)

2.4      Write FASTA file

Fourth step is to export DNA sequence to FATA file. writeFastaSR let users to write read in 'SangerRead' instance to file in FASTA format.

writeFastaSR(singleRead)

2.5      Generate Report

Fifth step is to create a static html report for 'SangerRead' instance by running generateReportSR function

generateReportSR(singleRead)

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SangerContig

'SangerContig' contains two lists of 'SangerRead' which are forward and reverse read list. It also contains alignment results and consensus read. It corresponds to a contig in Sanger sequencing.

3.1      Create **SangerContig** Instance

First step is to prepare all reads in the same directory and define the project parameters.

• inputFilesParentDir is the directory storing all raw ABIF files.
• contigName is the name of contigs. All targets share the same contig name.
• suffixForwardRegExp is the regular expression for forward read suffix.
• suffixReverseRegExp is the regular expression for reverse read suffix.

rawDataDir <- system.file("extdata", package = "sangeranalyseR")
inputFilesParentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "ACHLO")
contigName <- "Achl_ACHLO006-09"
suffixForwardRegExp <- "_[0-9]*_[F].ab1"
suffixReverseRegExp <- "_[0-9]*_[R].ab1"

After defining parameters, users can create 'SangerContig' instance by running SangerContig constructor function.

sangerContig <- SangerContig(parentDirectory      = inputFilesParentDir,
                             contigName           = contigName,
                             suffixForwardRegExp  = suffixForwardRegExp,
                             suffixReverseRegExp  = suffixReverseRegExp)

3.2      Launch Shiny App

Second step is to trigger 'SangerContig' Shiny app. In SangerContig constructor function, all forward and reverse reads in this contig share the same trimming parameter by default. It is inconvenient for users to check reads one by one through R command; therefore, we provide a local Shiny app to let users easily browse and change parameters in each read in the 'SangerContig' instance.

launchAppSC(sangerContig)

3.3      Write FASTA file

Third step is to export DNA sequence to FATA file. After changing trimming parameters in each read, users can run writeFastaSC function to write results into text file in FASTA format.

writeFastaSC(sangerContig)

3.4      Generate Report

Fourth step is to create a report. Users can create a static html report for the 'SangerContig' instance by running generateReportSC function.

generateReportSC(sangerContig)

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SangerAlignment

'SangerAlignment' contains a list of 'SangerContig' and the alignment results for all contigs. It corresponds to a rebuild DNA sequence fragment in Sanger sequencing.

4.1      Create **SangerAlignment** Instance

First step is to prepare all reads in the same directory and define the project parameters.

• inputFilesParentDir is the directory storing all raw ABIF files.
• suffixForwardRegExp is the regular expression for forward read suffix.
• suffixReverseRegExp is the regular expression for reverse read suffix.

rawDir <- system.file("extdata", package="sangeranalyseR")
parentDir <- file.path(rawDir, "Allolobophora_chlorotica", "RBNII")
suffixForwardRegExp <- "_[F]_[0-9]*.ab1"
suffixReverseRegExp <- "_[R]_[0-9]*.ab1"

Users can create 'SangerAlignment' instance by running SangerAlignment constructor function.

sangerAlignment <- 
        SangerAlignment(parentDirectory = parentDir,
                        suffixForwardRegExp = suffixForwardRegExp,
                        suffixReverseRegExp = suffixReverseRegExp,)

4.2      Launch Shiny App

Second step is to run launchAppSA to trigger the local 'SangerAlignment' Shiny app. Users can easily browse all 'SangerContig' instance in 'SangerAlignment' and change 'SangerRead' trimming parameters in each 'SangerContig' instance.

launchAppSA(sangerAlignment)

4.3      Write FASTA file

Third step is to run writeFastaSC function to write results into text file in FASTA format.

writeFastaSA(sangerAlignment)

4.4      Generate Report

Fourth step is to create a report. Users can create a static html report for the 'SangerAlignment' instance by running generateReportSA function.

generateReportSA(sangerAlignment)

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sangeranalyseR documentation built on Nov. 8, 2020, 5:59 p.m.