SangerRead-class: SangerRead

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

SangerRead

Description

An S4 class extending sangerseq S4 class which corresponds to a single ABIF file in Sanger sequencing.

Slots

objectResults

This is the object that stores all information of the creation result.

inputSource

The input source of the raw file. It must be "ABIF" or "FASTA". The default value is "ABIF".

readFeature

The direction of the Sanger read. The value must be "Forward Read" or "Reverse Read".

readFileName

The filename of the target input file.

fastaReadName

If inputSource is "FASTA", then this value has to be the name of the read inside the FASTA file; if inputSource is "ABIF", then this value is NULL by default.

geneticCode

Named character vector in the same format as GENETIC_CODE (the default), which represents the standard genetic code. This is the code with which the function will attempt to translate your DNA sequences. You can get an appropriate vector with the getGeneticCode() function. The default is the standard code.

abifRawData

An S4 class containing all fields in the ABIF file. It is the abif class defined in sangerseqR package.

QualityReport

A S4 class containing quality trimming related inputs and trimming results.

ChromatogramParam

A S4 class containing chromatogram inputs.

primaryAASeqS1

A polypeptide translated from primary DNA sequence starting from the first nucleic acid.

primaryAASeqS2

A polypeptide translated from primary DNA sequence starting from the second nucleic acid.

primaryAASeqS3

A polypeptide translated from primary DNA sequence starting from the third nucleic acid.

primarySeqRaw

The raw primary sequence from sangerseq class in sangerseqR package before base calling.

secondarySeqRaw

The raw secondary sequence from sangerseq class in sangerseqR package before base calling.

peakPosMatrixRaw

The raw peak position matrix from sangerseq class in sangerseqR package before base calling.

peakAmpMatrixRaw

The raw peak amplitude matrix from sangerseq class in sangerseqR package before base calling.

Author(s)

Kuan-Hao Chao

Examples

## Simple example
inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
A_chloroticaFFN <- file.path(inputFilesPath,
                             "Allolobophora_chlorotica",
                             "ACHLO",
                             "Achl_ACHLO006-09_1_F.ab1")
sangerReadF <- new("SangerRead",
                    readFeature           = "Forward Read",
                    readFileName          = A_chloroticaFFN)
                          
## Input From ABIF file format
# Forward Read
A_chloroticaFFN <- file.path(inputFilesPath,
                             "Allolobophora_chlorotica",
                             "ACHLO",
                             "Achl_ACHLO006-09_1_F.ab1")
sangerReadF <- new("SangerRead",
                    printLevel            = "SangerRead",
                    inputSource           = "ABIF",
                    readFeature           = "Forward Read",
                    readFileName          = A_chloroticaFFN,
                    fastaReadName         = NULL,
                    geneticCode           = GENETIC_CODE,
                    TrimmingMethod        = "M1",
                    M1TrimmingCutoff      = 0.0001,
                    M2CutoffQualityScore  = NULL,
                    M2SlidingWindowSize   = NULL,
                    baseNumPerRow         = 100,
                    heightPerRow          = 200,
                    signalRatioCutoff     = 0.33,
                    showTrimmed           = TRUE)

# Reverse Read
A_chloroticaRFN <- file.path(inputFilesPath,
                             "Allolobophora_chlorotica",
                             "ACHLO",
                             "Achl_ACHLO006-09_2_R.ab1")
sangerReadR <- new("SangerRead",
                    inputSource           = "ABIF",
                    readFeature           = "Reverse Read",
                    readFileName          = A_chloroticaRFN,
                    geneticCode           = GENETIC_CODE,
                    TrimmingMethod        = "M1",
                    M1TrimmingCutoff      = 0.0001,
                    M2CutoffQualityScore  = NULL,
                    M2SlidingWindowSize   = NULL,
                    baseNumPerRow         = 100,
                    heightPerRow          = 200,
                    signalRatioCutoff     = 0.33,
                    showTrimmed           = TRUE)


## Input From FASTA file format
# Forward Read
inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
A_chloroticaFFNfa <- file.path(inputFilesPath,
                               "fasta",
                               "SangerRead",
                               "Achl_ACHLO006-09_1_F.fa")
readNameFfa <- "Achl_ACHLO006-09_1_F"
sangerReadFfa <- new("SangerRead",
                     inputSource        = "FASTA",
                     readFeature        = "Forward Read",
                     readFileName       = A_chloroticaFFNfa,
                     fastaReadName      = readNameFfa,
                     geneticCode        = GENETIC_CODE)
# Reverse Read
A_chloroticaRFNfa <- file.path(inputFilesPath,
                               "fasta",
                               "SangerRead",
                               "Achl_ACHLO006-09_2_R.fa")
readNameRfa <- "Achl_ACHLO006-09_2_R"
sangerReadRfa <- new("SangerRead",
                     inputSource   = "FASTA",
                     readFeature   = "Reverse Read",
                     readFileName  = A_chloroticaRFNfa,
                     fastaReadName = readNameRfa,
                     geneticCode   = GENETIC_CODE)

roblanf/sangeranalyseR documentation built on April 15, 2024, 12:44 a.m.