SangerRead {sangeranalyseR} | R Documentation |
the wrapper function for SangerRead
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 )
inputSource |
The input source of the raw file. It must be |
readFeature |
The direction of the Sanger read. The value must be |
readFileName |
The filename of the target ABIF file. |
fastaReadName |
If |
geneticCode |
Named character vector in the same format as |
TrimmingMethod |
TrimmingMethod The read trimming method for this SangerRead. The value must be |
M1TrimmingCutoff |
The trimming cutoff for the Method 1. If |
M2CutoffQualityScore |
The trimming cutoff quality score for the Method 2. If |
M2SlidingWindowSize |
The trimming sliding window size for the Method 2. If |
baseNumPerRow |
It defines maximum base pairs in each row. The default value is |
heightPerRow |
It defines the height of each row in chromatogram. The default value is |
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 |
showTrimmed |
The logical value storing whether to show trimmed base pairs in chromatogram. The default value is |
A SangerRead instance.
Kuan-Hao Chao
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)