SangerRead-class {sangeranalyseR} | R Documentation

## SangerRead

### Description

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

### Slots

`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. It can be `"ABIF"` or `"FASTA"` 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.

`abifRawData`

  A S4 class containing all fields in the ABIF file. It is 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.

`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.

`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

    ## Input From ABIF file format
    # Forward Read
    inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
    A_chloroticaFFN <- file.path(inputFilesPath,
                                 "Allolobophora_chlorotica",
                                 "ACHLO",
                                 "Achl_ACHLO006-09_1_F.ab1")
    sangerReadF <- new("SangerRead",
                        inputSource           = "ABIF",
                        readFeature           = "Forward Read",
                        readFileName          = A_chloroticaFFN,
                        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)

[Package sangeranalyseR version 1.2.0 Index]