SangerRead: SangerRead

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

SangerRead

Description

the wrapper function for SangerRead

Usage

SangerRead(
  printLevel = "SangerRead",
  inputSource = "ABIF",
  readFeature = "",
  readFileName = "",
  fastaReadName = NULL,
  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". M1 is the modified Mott's trimming algorithm that can also be found in Phred/Phrap and Biopython. M2 is like trimmomatic's sliding window method.
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

inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
A_chloroticaFdFN <- file.path(inputFilesPath,
                              "Allolobophora_chlorotica",
                              "ACHLO",
                              "Achl_ACHLO006-09_1_F.ab1")
sangerRead <- SangerRead(
                   printLevel            = "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)

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