SangerRead: SangerRead

Description Usage Arguments Value Author(s) Examples

View source: R/Constructors.R

Description

the wrapper function for SangerRead

Usage

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SangerRead(inputSource = "ABIF", readFeature = "", readFileName = "",
  fastaReadName = "", geneticCode = GENETIC_CODE,
  TrimmingMethod = "M1", M1TrimmingCutoff = 1e-04,
  M2CutoffQualityScore = NULL, M2SlidingWindowSize = NULL,
  baseNumPerRow = 100, heightPerRow = 200, signalRatioCutoff = 0.33,
  showTrimmed = TRUE)

Arguments

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 ABIF 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 "" 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.

TrimmingMethod

TrimmingMethod The read trimming method for this SangerRead. The value must be "M1" (the default) or 'M2'.

M1TrimmingCutoff

The trimming cutoff for the Method 1. If TrimmingMethod is "M1", then the default value is 0.0001. Otherwise, the value must be NULL.

M2CutoffQualityScore

The trimming cutoff quality score for the Method 2. If TrimmingMethod is 'M2', then the default value is 20. Otherwise, the value must be NULL. It works with M2SlidingWindowSize.

M2SlidingWindowSize

The trimming sliding window size for the Method 2. If TrimmingMethod is 'M2', then the default value is 10. Otherwise, the value must be NULL. It works with M2CutoffQualityScore.

baseNumPerRow

It defines maximum base pairs in each row. The default value is 100.

heightPerRow

It defines the height of each row in chromatogram. The default value is 200.

signalRatioCutoff

The ratio of the height of a secondary peak to a primary peak. Secondary peaks higher than this ratio are annotated. Those below the ratio are excluded. The default value is 0.33.

showTrimmed

The logical value storing whether to show trimmed base pairs in chromatogram. The default value is TRUE.

Value

A SangerRead instance.

Author(s)

Kuan-Hao Chao

Examples

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inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
A_chloroticaFdFN <- file.path(inputFilesPath,
                              "Allolobophora_chlorotica",
                              "ACHLO",
                              "Achl_ACHLO006-09_1_F.ab1")
sangerRead <- SangerRead(
                   inputSource           = "ABIF",
                   readFeature           = "Forward Read",
                   readFileName          = A_chloroticaFdFN,
                   geneticCode           = GENETIC_CODE,
                   TrimmingMethod        = "M1",
                   M1TrimmingCutoff      = 0.0001,
                   M2CutoffQualityScore  = NULL,
                   M2SlidingWindowSize   = NULL,
                   baseNumPerRow         = 100,
                   heightPerRow          = 200,
                   signalRatioCutoff     = 0.33,
                   showTrimmed           = TRUE)

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