R/Constructors.R
In roblanf/sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Defines functions
SangerRead
SangerContig
SangerAlignment
Documented in
SangerAlignment
SangerContig
SangerRead
### ============================================================================
### Self-defined constructor for AlignedConsensusSet
### ============================================================================
#' @description the wrapper function for SangerAlignment
#'
#' @param inputSource The input source of the raw file. It must be \code{"ABIF"} or \code{"FASTA"}. The default value is \code{"ABIF"}.
#' @param FASTA_File If \code{inputSource} is \code{"FASTA"}, then this value has to be the name of the FASTA file; if \code{inputSource} is \code{"ABIF"}, then this value is \code{""} by default.
#' @param CSV_NamesConversion The file path to the CSV file that provides read names that follow the naming regulation. If \code{inputSource} is \code{"FASTA"}, then users need to prepare the csv file or make sure the original names inside FASTA file are valid; if \code{inputSource} is \code{"ABIF"}, then this value is \code{NULL} by default.
#' @param ABIF_Directory The parent directory of all of the reads contained in ABIF format you wish to analyse. In SangerAlignment, all reads in subdirectories will be scanned recursively.
#' @param REGEX_SuffixForward The suffix of the filenames for forward reads in regular expression, i.e. reads that do not need to be reverse-complemented. For forward reads, it should be \code{"_F.ab1"}.
#' @param REGEX_SuffixReverse The suffix of the filenames for reverse reads in regular expression, i.e. reads that need to be reverse-complemented. For revcerse reads, it should be \code{"_R.ab1"}.
#' @param TrimmingMethod TrimmingMethod The read trimming method for this SangerRead. The value must be \code{"M1"} (the default) or \code{'M2'}.
#' @param M1TrimmingCutoff The trimming cutoff for the Method 1. If \code{TrimmingMethod} is \code{"M1"}, then the default value is \code{0.0001}. Otherwise, the value must be \code{NULL}.
#' @param M2CutoffQualityScore The trimming cutoff quality score for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{20}. Otherwise, the value must be \code{NULL}. It works with \code{M2SlidingWindowSize}.
#' @param M2SlidingWindowSize The trimming sliding window size for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{10}. Otherwise, the value must be \code{NULL}. It works with \code{M2CutoffQualityScore}.
#' @param baseNumPerRow It defines maximum base pairs in each row. The default value is \code{100}.
#' @param heightPerRow It defines the height of each row in chromatogram. The default value is \code{200}.
#' @param 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 \code{0.33}.
#' @param showTrimmed The logical value storing whether to show trimmed base pairs in chromatogram. The default value is \code{TRUE}.
#' @param refAminoAcidSeq An amino acid reference sequence supplied as a string or an AAString object. If your sequences are protein-coding DNA seuqences, and you want to have frameshifts automatically detected and corrected, supply a reference amino acid sequence via this argument. If this argument is supplied, the sequences are then kept in frame for the alignment step. Fwd sequences are assumed to come from the sense (i.e. coding, or "+") strand. The default value is \code{""}.
#' @param minReadsNum The minimum number of reads required to make a consensus sequence, must be 2 or more. The default value is \code{2}.
#' @param minReadLength Reads shorter than this will not be included in the readset. The default \code{20} means that all reads with length of 20 or more will be included. Note that this is the length of a read after it has been trimmed.
#' @param minFractionCall Minimum fraction of the sequences required to call a consensus sequence for SangerContig at any given position (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.75 implying that 3/4 of all reads must be present in order to call a consensus.
#' @param maxFractionLost Numeric giving the maximum fraction of sequence information that can be lost in the consensus sequence for SangerContig (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.5, implying that each consensus base can ignore at most 50 percent of the information at a given position.
#' @param geneticCode Named character vector in the same format as \code{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.
#' @param acceptStopCodons The logical value \code{TRUE} or \code{FALSE}. \code{TRUE} (the defualt): keep all reads, regardless of whether they have stop codons; \code{FALSE}: reject reads with stop codons. If \code{FALSE} is selected, then the number of stop codons is calculated after attempting to correct frameshift mutations (if applicable).
#' @param readingFrame \code{1}, \code{2}, or \code{3}. Only used if \code{accept.stop.codons == FALSE}. This specifies the reading frame that is used to determine stop codons. If you use a \code{refAminoAcidSeq}, then the frame should always be \code{1}, since all reads will be shifted to frame 1 during frameshift correction. Otherwise, you should select the appropriate reading frame.
#' @param minFractionCallSA Minimum fraction of the sequences required to call a consensus sequence for SangerAlignment at any given position (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.75 implying that 3/4 of all reads must be present in order to call a consensus.
#' @param maxFractionLostSA Numeric giving the maximum fraction of sequence information that can be lost in the consensus sequence for SangerAlignment (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.5, implying that each consensus base can ignore at most 50 percent of the information at a given position.
#' @param processorsNum The number of processors to use, or NULL (the default) for all available processors.
#'
#' @title SangerAlignment
#' @name SangerAlignment
#' @export
#'
#' @return A SangerAlignment instance.
#'
#' @author Kuan-Hao Chao
#' @examples
#' rawDataDir <- system.file("extdata", package = "sangeranalyseR")
#' parentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "RBNII")
#' REGEX_SuffixForward <- "_[0-9]*_F.ab1$"
#' REGEX_SuffixReverse <- "_[0-9]*_R.ab1$"
#' sangerAlignment <- SangerAlignment(
#' inputSource = "ABIF",
#' ABIF_Directory = parentDir,
#' REGEX_SuffixForward = REGEX_SuffixForward,
#' REGEX_SuffixReverse = REGEX_SuffixReverse,
#' refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
#' TrimmingMethod = "M1",
#' M1TrimmingCutoff = 0.0001,
#' M2CutoffQualityScore = NULL,
#' M2SlidingWindowSize = NULL,
#' baseNumPerRow = 100,
#' heightPerRow = 200,
#' signalRatioCutoff = 0.33,
#' showTrimmed = TRUE,
#' processorsNum = 2)
SangerAlignment <- function(printLevel = "SangerAlignment",
inputSource = "ABIF",
processMethod = "REGEX",
ABIF_Directory = NULL,
FASTA_File = NULL,
REGEX_SuffixForward = NULL,
REGEX_SuffixReverse = NULL,
CSV_NamesConversion = NULL,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
refAminoAcidSeq = "",
minReadsNum = 2,
minReadLength = 20,
minFractionCall = 0.5,
maxFractionLost = 0.5,
acceptStopCodons = TRUE,
readingFrame = 1,
processorsNum = 1) {
newAlignment <- new("SangerAlignment",
inputSource = inputSource,
processMethod = processMethod,
ABIF_Directory = ABIF_Directory,
FASTA_File = FASTA_File,
REGEX_SuffixForward = REGEX_SuffixForward,
REGEX_SuffixReverse = REGEX_SuffixReverse,
CSV_NamesConversion = CSV_NamesConversion,
geneticCode = geneticCode,
TrimmingMethod = TrimmingMethod,
M1TrimmingCutoff = M1TrimmingCutoff,
M2CutoffQualityScore = M2CutoffQualityScore,
M2SlidingWindowSize = M2SlidingWindowSize,
baseNumPerRow = baseNumPerRow,
heightPerRow = heightPerRow,
signalRatioCutoff = signalRatioCutoff,
showTrimmed = showTrimmed,
refAminoAcidSeq = refAminoAcidSeq,
minReadsNum = minReadsNum,
minReadLength = minReadLength,
minFractionCall = minFractionCall,
maxFractionLost = maxFractionLost,
acceptStopCodons = acceptStopCodons,
readingFrame = readingFrame,
processorsNum = processorsNum)
return(newAlignment)
}
### ============================================================================
### Self-defined constructor for SangerContig
### ============================================================================
#' @description the wrapper function for SangerContig
#'
#' @param inputSource The input source of the raw file. It must be \code{"ABIF"} or \code{"FASTA"}. The default value is \code{"ABIF"}.
#' @param FASTA_File If \code{inputSource} is \code{"FASTA"}, then this value has to be the name of the FASTA file; if \code{inputSource} is \code{"ABIF"}, then this value is \code{""} by default.
#' @param CSV_NamesConversion The file path to the CSV file that provides read names that follow the naming regulation. If \code{inputSource} is \code{"FASTA"}, then users need to prepare the csv file or make sure the original names inside FASTA file are valid; if \code{inputSource} is \code{"ABIF"}, then this value is \code{NULL} by default.
#' @param ABIF_Directory The parent directory of all of the reads contained in ABIF format you wish to analyse. In SangerContig, all reads must be in the first layer in this directory.
#' @param contigName The contig name of all the reads in \code{ABIF_Directory}.
#' @param REGEX_SuffixForward The suffix of the filenames for forward reads in regular expression, i.e. reads that do not need to be reverse-complemented. For forward reads, it should be \code{"_F.ab1"}.
#' @param REGEX_SuffixReverse The suffix of the filenames for reverse reads in regular expression, i.e. reads that need to be reverse-complemented. For revcerse reads, it should be \code{"_R.ab1"}.
#' @param TrimmingMethod TrimmingMethod The read trimming method for this SangerRead. The value must be \code{"M1"} (the default) or \code{'M2'}.
#' @param M1TrimmingCutoff The trimming cutoff for the Method 1. If \code{TrimmingMethod} is \code{"M1"}, then the default value is \code{0.0001}. Otherwise, the value must be \code{NULL}.
#' @param M2CutoffQualityScore The trimming cutoff quality score for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{20}. Otherwise, the value must be \code{NULL}. It works with \code{M2SlidingWindowSize}.
#' @param M2SlidingWindowSize The trimming sliding window size for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{10}. Otherwise, the value must be \code{NULL}. It works with \code{M2CutoffQualityScore}.
#' @param baseNumPerRow It defines maximum base pairs in each row. The default value is \code{100}.
#' @param heightPerRow It defines the height of each row in chromatogram. The default value is \code{200}.
#' @param 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 \code{0.33}.
#' @param showTrimmed The logical value storing whether to show trimmed base pairs in chromatogram. The default value is \code{TRUE}.
#' @param refAminoAcidSeq An amino acid reference sequence supplied as a string or an AAString object. If your sequences are protein-coding DNA seuqences, and you want to have frameshifts automatically detected and corrected, supply a reference amino acid sequence via this argument. If this argument is supplied, the sequences are then kept in frame for the alignment step. Fwd sequences are assumed to come from the sense (i.e. coding, or "+") strand. The default value is \code{""}.
#' @param minReadsNum The minimum number of reads required to make a consensus sequence, must be 2 or more. The default value is \code{2}.
#' @param minReadLength Reads shorter than this will not be included in the readset. The default \code{20} means that all reads with length of 20 or more will be included. Note that this is the length of a read after it has been trimmed.
#' @param minFractionCall Minimum fraction of the sequences required to call a consensus sequence for SangerContig at any given position (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.75 implying that 3/4 of all reads must be present in order to call a consensus.
#' @param maxFractionLost Numeric giving the maximum fraction of sequence information that can be lost in the consensus sequence for SangerContig (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.5, implying that each consensus base can ignore at most 50 percent of the information at a given position.
#' @param geneticCode Named character vector in the same format as \code{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.
#' @param acceptStopCodons The logical value \code{TRUE} or \code{FALSE}. \code{TRUE} (the defualt): keep all reads, regardless of whether they have stop codons; \code{FALSE}: reject reads with stop codons. If \code{FALSE} is selected, then the number of stop codons is calculated after attempting to correct frameshift mutations (if applicable).
#' @param readingFrame \code{1}, \code{2}, or \code{3}. Only used if \code{accept.stop.codons == FALSE}. This specifies the reading frame that is used to determine stop codons. If you use a \code{refAminoAcidSeq}, then the frame should always be \code{1}, since all reads will be shifted to frame 1 during frameshift correction. Otherwise, you should select the appropriate reading frame.
#' @param processorsNum The number of processors to use, or NULL (the default) for all available processors.
#'
#' @title SangerContig
#' @name SangerContig
#' @export
#'
#' @return A SangerContig instance.
#'
#' @author Kuan-Hao Chao
#' @examples
#' rawDataDir <- system.file("extdata", package = "sangeranalyseR")
#' parentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "ACHLO")
#' contigName <- "Achl_ACHLO006-09"
#' REGEX_SuffixForward <- "_F.ab1"
#' REGEX_SuffixReverse <- "_R.ab1"
#' sangerContig <- SangerContig(
#' inputSource = "ABIF",
#' ABIF_Directory = parentDir,
#' contigName = contigName,
#' REGEX_SuffixForward = REGEX_SuffixForward,
#' REGEX_SuffixReverse = REGEX_SuffixReverse,
#' refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
#' TrimmingMethod = "M2",
#' M1TrimmingCutoff = NULL,
#' M2CutoffQualityScore = 20,
#' M2SlidingWindowSize = 10,
#' baseNumPerRow = 100,
#' heightPerRow = 200,
#' signalRatioCutoff = 0.33,
#' showTrimmed = TRUE,
#' processorsNum = 2)
SangerContig <- function(printLevel = "SangerContig",
inputSource = "ABIF",
processMethod = "REGEX",
ABIF_Directory = NULL,
FASTA_File = NULL,
REGEX_SuffixForward = NULL,
REGEX_SuffixReverse = NULL,
CSV_NamesConversion = NULL,
contigName = NULL,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
refAminoAcidSeq = "",
minReadsNum = 2,
minReadLength = 20,
minFractionCall = 0.5,
maxFractionLost = 0.5,
acceptStopCodons = TRUE,
readingFrame = 1,
processorsNum = 1) {
newContig <- new("SangerContig",
printLevel = printLevel,
inputSource = inputSource,
processMethod = processMethod,
ABIF_Directory = ABIF_Directory,
FASTA_File = FASTA_File,
REGEX_SuffixForward = REGEX_SuffixForward,
REGEX_SuffixReverse = REGEX_SuffixReverse,
CSV_NamesConversion = CSV_NamesConversion,
contigName = contigName,
geneticCode = geneticCode,
TrimmingMethod = TrimmingMethod,
M1TrimmingCutoff = M1TrimmingCutoff,
M2CutoffQualityScore = M2CutoffQualityScore,
M2SlidingWindowSize = M2SlidingWindowSize,
baseNumPerRow = baseNumPerRow,
heightPerRow = heightPerRow,
signalRatioCutoff = signalRatioCutoff,
showTrimmed = showTrimmed,
refAminoAcidSeq = refAminoAcidSeq,
minReadsNum = minReadsNum,
minReadLength = minReadLength,
minFractionCall = minFractionCall,
maxFractionLost = maxFractionLost,
acceptStopCodons = acceptStopCodons,
readingFrame = readingFrame,
processorsNum = processorsNum)
return(newContig)
}
### ============================================================================
### Self-defined constructor for SangerRead
### ============================================================================
#' @description the wrapper function for SangerRead
#'
#' @param inputSource The input source of the raw file. It must be \code{"ABIF"} or \code{"FASTA"}. The default value is \code{"ABIF"}.
#' @param readFeature The direction of the Sanger read. The value must be \code{"Forward Read"} or \code{"Reverse Read"}.
#' @param readFileName The filename of the target ABIF file.
#' @param fastaReadName If \code{inputSource} is \code{"FASTA"}, then this value has to be the name of the read inside the FASTA file; if \code{inputSource} is \code{"ABIF"}, then this value is \code{""} by default.
#' @param geneticCode Named character vector in the same format as \code{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.
#' @param TrimmingMethod TrimmingMethod The read trimming method for this SangerRead. The value must be \code{"M1"} (the default) or \code{"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.
#' @param M1TrimmingCutoff The trimming cutoff for the Method 1. If \code{TrimmingMethod} is \code{"M1"}, then the default value is \code{0.0001}. Otherwise, the value must be \code{NULL}.
#' @param M2CutoffQualityScore The trimming cutoff quality score for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{20}. Otherwise, the value must be \code{NULL}. It works with \code{M2SlidingWindowSize}.
#' @param M2SlidingWindowSize The trimming sliding window size for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{10}. Otherwise, the value must be \code{NULL}. It works with \code{M2CutoffQualityScore}.
#' @param baseNumPerRow It defines maximum base pairs in each row. The default value is \code{100}.
#' @param heightPerRow It defines the height of each row in chromatogram. The default value is \code{200}.
#' @param 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 \code{0.33}.
#' @param showTrimmed The logical value storing whether to show trimmed base pairs in chromatogram. The default value is \code{TRUE}.
#'
#' @title SangerRead
#' @name SangerRead
#' @export
#'
#' @return A SangerRead instance.
#'
#' @author 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)
SangerRead <- function(printLevel = "SangerRead",
inputSource = "ABIF",
readFeature = "",
readFileName = "",
fastaReadName = NULL,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE) {
newRead <- new("SangerRead",
printLevel = printLevel,
inputSource = inputSource,
readFeature = readFeature,
readFileName = readFileName,
fastaReadName = fastaReadName,
geneticCode = geneticCode,
TrimmingMethod = TrimmingMethod,
M1TrimmingCutoff = M1TrimmingCutoff,
M2CutoffQualityScore = M2CutoffQualityScore,
M2SlidingWindowSize = M2SlidingWindowSize,
baseNumPerRow = baseNumPerRow,
heightPerRow = heightPerRow,
signalRatioCutoff = signalRatioCutoff,
showTrimmed = showTrimmed)
return(newRead)
}
roblanf/sangeranalyseR documentation built on April 15, 2024, 12:44 a.m.
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Defines functions SangerRead SangerContig SangerAlignment
Documented in SangerAlignment SangerContig SangerRead
### ============================================================================
### Self-defined constructor for AlignedConsensusSet
### ============================================================================
#' @description the wrapper function for SangerAlignment
#'
#' @param inputSource The input source of the raw file. It must be \code{"ABIF"} or \code{"FASTA"}. The default value is \code{"ABIF"}.
#' @param FASTA_File If \code{inputSource} is \code{"FASTA"}, then this value has to be the name of the FASTA file; if \code{inputSource} is \code{"ABIF"}, then this value is \code{""} by default.
#' @param CSV_NamesConversion The file path to the CSV file that provides read names that follow the naming regulation. If \code{inputSource} is \code{"FASTA"}, then users need to prepare the csv file or make sure the original names inside FASTA file are valid; if \code{inputSource} is \code{"ABIF"}, then this value is \code{NULL} by default.
#' @param ABIF_Directory The parent directory of all of the reads contained in ABIF format you wish to analyse. In SangerAlignment, all reads in subdirectories will be scanned recursively.
#' @param REGEX_SuffixForward The suffix of the filenames for forward reads in regular expression, i.e. reads that do not need to be reverse-complemented. For forward reads, it should be \code{"_F.ab1"}.
#' @param REGEX_SuffixReverse The suffix of the filenames for reverse reads in regular expression, i.e. reads that need to be reverse-complemented. For revcerse reads, it should be \code{"_R.ab1"}.
#' @param TrimmingMethod TrimmingMethod The read trimming method for this SangerRead. The value must be \code{"M1"} (the default) or \code{'M2'}.
#' @param M1TrimmingCutoff The trimming cutoff for the Method 1. If \code{TrimmingMethod} is \code{"M1"}, then the default value is \code{0.0001}. Otherwise, the value must be \code{NULL}.
#' @param M2CutoffQualityScore The trimming cutoff quality score for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{20}. Otherwise, the value must be \code{NULL}. It works with \code{M2SlidingWindowSize}.
#' @param M2SlidingWindowSize The trimming sliding window size for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{10}. Otherwise, the value must be \code{NULL}. It works with \code{M2CutoffQualityScore}.
#' @param baseNumPerRow It defines maximum base pairs in each row. The default value is \code{100}.
#' @param heightPerRow It defines the height of each row in chromatogram. The default value is \code{200}.
#' @param 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 \code{0.33}.
#' @param showTrimmed The logical value storing whether to show trimmed base pairs in chromatogram. The default value is \code{TRUE}.
#' @param refAminoAcidSeq An amino acid reference sequence supplied as a string or an AAString object. If your sequences are protein-coding DNA seuqences, and you want to have frameshifts automatically detected and corrected, supply a reference amino acid sequence via this argument. If this argument is supplied, the sequences are then kept in frame for the alignment step. Fwd sequences are assumed to come from the sense (i.e. coding, or "+") strand. The default value is \code{""}.
#' @param minReadsNum The minimum number of reads required to make a consensus sequence, must be 2 or more. The default value is \code{2}.
#' @param minReadLength Reads shorter than this will not be included in the readset. The default \code{20} means that all reads with length of 20 or more will be included. Note that this is the length of a read after it has been trimmed.
#' @param minFractionCall Minimum fraction of the sequences required to call a consensus sequence for SangerContig at any given position (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.75 implying that 3/4 of all reads must be present in order to call a consensus.
#' @param maxFractionLost Numeric giving the maximum fraction of sequence information that can be lost in the consensus sequence for SangerContig (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.5, implying that each consensus base can ignore at most 50 percent of the information at a given position.
#' @param geneticCode Named character vector in the same format as \code{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.
#' @param acceptStopCodons The logical value \code{TRUE} or \code{FALSE}. \code{TRUE} (the defualt): keep all reads, regardless of whether they have stop codons; \code{FALSE}: reject reads with stop codons. If \code{FALSE} is selected, then the number of stop codons is calculated after attempting to correct frameshift mutations (if applicable).
#' @param readingFrame \code{1}, \code{2}, or \code{3}. Only used if \code{accept.stop.codons == FALSE}. This specifies the reading frame that is used to determine stop codons. If you use a \code{refAminoAcidSeq}, then the frame should always be \code{1}, since all reads will be shifted to frame 1 during frameshift correction. Otherwise, you should select the appropriate reading frame.
#' @param minFractionCallSA Minimum fraction of the sequences required to call a consensus sequence for SangerAlignment at any given position (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.75 implying that 3/4 of all reads must be present in order to call a consensus.
#' @param maxFractionLostSA Numeric giving the maximum fraction of sequence information that can be lost in the consensus sequence for SangerAlignment (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.5, implying that each consensus base can ignore at most 50 percent of the information at a given position.
#' @param processorsNum The number of processors to use, or NULL (the default) for all available processors.
#'
#' @title SangerAlignment
#' @name SangerAlignment
#' @export
#'
#' @return A SangerAlignment instance.
#'
#' @author Kuan-Hao Chao
#' @examples
#' rawDataDir <- system.file("extdata", package = "sangeranalyseR")
#' parentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "RBNII")
#' REGEX_SuffixForward <- "_[0-9]*_F.ab1$"
#' REGEX_SuffixReverse <- "_[0-9]*_R.ab1$"
#' sangerAlignment <- SangerAlignment(
#' inputSource = "ABIF",
#' ABIF_Directory = parentDir,
#' REGEX_SuffixForward = REGEX_SuffixForward,
#' REGEX_SuffixReverse = REGEX_SuffixReverse,
#' refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
#' TrimmingMethod = "M1",
#' M1TrimmingCutoff = 0.0001,
#' M2CutoffQualityScore = NULL,
#' M2SlidingWindowSize = NULL,
#' baseNumPerRow = 100,
#' heightPerRow = 200,
#' signalRatioCutoff = 0.33,
#' showTrimmed = TRUE,
#' processorsNum = 2)
SangerAlignment <- function(printLevel = "SangerAlignment",
inputSource = "ABIF",
processMethod = "REGEX",
ABIF_Directory = NULL,
FASTA_File = NULL,
REGEX_SuffixForward = NULL,
REGEX_SuffixReverse = NULL,
CSV_NamesConversion = NULL,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
refAminoAcidSeq = "",
minReadsNum = 2,
minReadLength = 20,
minFractionCall = 0.5,
maxFractionLost = 0.5,
acceptStopCodons = TRUE,
readingFrame = 1,
processorsNum = 1) {
newAlignment <- new("SangerAlignment",
inputSource = inputSource,
processMethod = processMethod,
ABIF_Directory = ABIF_Directory,
FASTA_File = FASTA_File,
REGEX_SuffixForward = REGEX_SuffixForward,
REGEX_SuffixReverse = REGEX_SuffixReverse,
CSV_NamesConversion = CSV_NamesConversion,
geneticCode = geneticCode,
TrimmingMethod = TrimmingMethod,
M1TrimmingCutoff = M1TrimmingCutoff,
M2CutoffQualityScore = M2CutoffQualityScore,
M2SlidingWindowSize = M2SlidingWindowSize,
baseNumPerRow = baseNumPerRow,
heightPerRow = heightPerRow,
signalRatioCutoff = signalRatioCutoff,
showTrimmed = showTrimmed,
refAminoAcidSeq = refAminoAcidSeq,
minReadsNum = minReadsNum,
minReadLength = minReadLength,
minFractionCall = minFractionCall,
maxFractionLost = maxFractionLost,
acceptStopCodons = acceptStopCodons,
readingFrame = readingFrame,
processorsNum = processorsNum)
return(newAlignment)
}
### ============================================================================
### Self-defined constructor for SangerContig
### ============================================================================
#' @description the wrapper function for SangerContig
#'
#' @param inputSource The input source of the raw file. It must be \code{"ABIF"} or \code{"FASTA"}. The default value is \code{"ABIF"}.
#' @param FASTA_File If \code{inputSource} is \code{"FASTA"}, then this value has to be the name of the FASTA file; if \code{inputSource} is \code{"ABIF"}, then this value is \code{""} by default.
#' @param CSV_NamesConversion The file path to the CSV file that provides read names that follow the naming regulation. If \code{inputSource} is \code{"FASTA"}, then users need to prepare the csv file or make sure the original names inside FASTA file are valid; if \code{inputSource} is \code{"ABIF"}, then this value is \code{NULL} by default.
#' @param ABIF_Directory The parent directory of all of the reads contained in ABIF format you wish to analyse. In SangerContig, all reads must be in the first layer in this directory.
#' @param contigName The contig name of all the reads in \code{ABIF_Directory}.
#' @param REGEX_SuffixForward The suffix of the filenames for forward reads in regular expression, i.e. reads that do not need to be reverse-complemented. For forward reads, it should be \code{"_F.ab1"}.
#' @param REGEX_SuffixReverse The suffix of the filenames for reverse reads in regular expression, i.e. reads that need to be reverse-complemented. For revcerse reads, it should be \code{"_R.ab1"}.
#' @param TrimmingMethod TrimmingMethod The read trimming method for this SangerRead. The value must be \code{"M1"} (the default) or \code{'M2'}.
#' @param M1TrimmingCutoff The trimming cutoff for the Method 1. If \code{TrimmingMethod} is \code{"M1"}, then the default value is \code{0.0001}. Otherwise, the value must be \code{NULL}.
#' @param M2CutoffQualityScore The trimming cutoff quality score for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{20}. Otherwise, the value must be \code{NULL}. It works with \code{M2SlidingWindowSize}.
#' @param M2SlidingWindowSize The trimming sliding window size for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{10}. Otherwise, the value must be \code{NULL}. It works with \code{M2CutoffQualityScore}.
#' @param baseNumPerRow It defines maximum base pairs in each row. The default value is \code{100}.
#' @param heightPerRow It defines the height of each row in chromatogram. The default value is \code{200}.
#' @param 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 \code{0.33}.
#' @param showTrimmed The logical value storing whether to show trimmed base pairs in chromatogram. The default value is \code{TRUE}.
#' @param refAminoAcidSeq An amino acid reference sequence supplied as a string or an AAString object. If your sequences are protein-coding DNA seuqences, and you want to have frameshifts automatically detected and corrected, supply a reference amino acid sequence via this argument. If this argument is supplied, the sequences are then kept in frame for the alignment step. Fwd sequences are assumed to come from the sense (i.e. coding, or "+") strand. The default value is \code{""}.
#' @param minReadsNum The minimum number of reads required to make a consensus sequence, must be 2 or more. The default value is \code{2}.
#' @param minReadLength Reads shorter than this will not be included in the readset. The default \code{20} means that all reads with length of 20 or more will be included. Note that this is the length of a read after it has been trimmed.
#' @param minFractionCall Minimum fraction of the sequences required to call a consensus sequence for SangerContig at any given position (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.75 implying that 3/4 of all reads must be present in order to call a consensus.
#' @param maxFractionLost Numeric giving the maximum fraction of sequence information that can be lost in the consensus sequence for SangerContig (see the ConsensusSequence() function from DECIPHER for more information). Defaults to 0.5, implying that each consensus base can ignore at most 50 percent of the information at a given position.
#' @param geneticCode Named character vector in the same format as \code{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.
#' @param acceptStopCodons The logical value \code{TRUE} or \code{FALSE}. \code{TRUE} (the defualt): keep all reads, regardless of whether they have stop codons; \code{FALSE}: reject reads with stop codons. If \code{FALSE} is selected, then the number of stop codons is calculated after attempting to correct frameshift mutations (if applicable).
#' @param readingFrame \code{1}, \code{2}, or \code{3}. Only used if \code{accept.stop.codons == FALSE}. This specifies the reading frame that is used to determine stop codons. If you use a \code{refAminoAcidSeq}, then the frame should always be \code{1}, since all reads will be shifted to frame 1 during frameshift correction. Otherwise, you should select the appropriate reading frame.
#' @param processorsNum The number of processors to use, or NULL (the default) for all available processors.
#'
#' @title SangerContig
#' @name SangerContig
#' @export
#'
#' @return A SangerContig instance.
#'
#' @author Kuan-Hao Chao
#' @examples
#' rawDataDir <- system.file("extdata", package = "sangeranalyseR")
#' parentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "ACHLO")
#' contigName <- "Achl_ACHLO006-09"
#' REGEX_SuffixForward <- "_F.ab1"
#' REGEX_SuffixReverse <- "_R.ab1"
#' sangerContig <- SangerContig(
#' inputSource = "ABIF",
#' ABIF_Directory = parentDir,
#' contigName = contigName,
#' REGEX_SuffixForward = REGEX_SuffixForward,
#' REGEX_SuffixReverse = REGEX_SuffixReverse,
#' refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
#' TrimmingMethod = "M2",
#' M1TrimmingCutoff = NULL,
#' M2CutoffQualityScore = 20,
#' M2SlidingWindowSize = 10,
#' baseNumPerRow = 100,
#' heightPerRow = 200,
#' signalRatioCutoff = 0.33,
#' showTrimmed = TRUE,
#' processorsNum = 2)
SangerContig <- function(printLevel = "SangerContig",
inputSource = "ABIF",
processMethod = "REGEX",
ABIF_Directory = NULL,
FASTA_File = NULL,
REGEX_SuffixForward = NULL,
REGEX_SuffixReverse = NULL,
CSV_NamesConversion = NULL,
contigName = NULL,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE,
refAminoAcidSeq = "",
minReadsNum = 2,
minReadLength = 20,
minFractionCall = 0.5,
maxFractionLost = 0.5,
acceptStopCodons = TRUE,
readingFrame = 1,
processorsNum = 1) {
newContig <- new("SangerContig",
printLevel = printLevel,
inputSource = inputSource,
processMethod = processMethod,
ABIF_Directory = ABIF_Directory,
FASTA_File = FASTA_File,
REGEX_SuffixForward = REGEX_SuffixForward,
REGEX_SuffixReverse = REGEX_SuffixReverse,
CSV_NamesConversion = CSV_NamesConversion,
contigName = contigName,
geneticCode = geneticCode,
TrimmingMethod = TrimmingMethod,
M1TrimmingCutoff = M1TrimmingCutoff,
M2CutoffQualityScore = M2CutoffQualityScore,
M2SlidingWindowSize = M2SlidingWindowSize,
baseNumPerRow = baseNumPerRow,
heightPerRow = heightPerRow,
signalRatioCutoff = signalRatioCutoff,
showTrimmed = showTrimmed,
refAminoAcidSeq = refAminoAcidSeq,
minReadsNum = minReadsNum,
minReadLength = minReadLength,
minFractionCall = minFractionCall,
maxFractionLost = maxFractionLost,
acceptStopCodons = acceptStopCodons,
readingFrame = readingFrame,
processorsNum = processorsNum)
return(newContig)
}
### ============================================================================
### Self-defined constructor for SangerRead
### ============================================================================
#' @description the wrapper function for SangerRead
#'
#' @param inputSource The input source of the raw file. It must be \code{"ABIF"} or \code{"FASTA"}. The default value is \code{"ABIF"}.
#' @param readFeature The direction of the Sanger read. The value must be \code{"Forward Read"} or \code{"Reverse Read"}.
#' @param readFileName The filename of the target ABIF file.
#' @param fastaReadName If \code{inputSource} is \code{"FASTA"}, then this value has to be the name of the read inside the FASTA file; if \code{inputSource} is \code{"ABIF"}, then this value is \code{""} by default.
#' @param geneticCode Named character vector in the same format as \code{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.
#' @param TrimmingMethod TrimmingMethod The read trimming method for this SangerRead. The value must be \code{"M1"} (the default) or \code{"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.
#' @param M1TrimmingCutoff The trimming cutoff for the Method 1. If \code{TrimmingMethod} is \code{"M1"}, then the default value is \code{0.0001}. Otherwise, the value must be \code{NULL}.
#' @param M2CutoffQualityScore The trimming cutoff quality score for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{20}. Otherwise, the value must be \code{NULL}. It works with \code{M2SlidingWindowSize}.
#' @param M2SlidingWindowSize The trimming sliding window size for the Method 2. If \code{TrimmingMethod} is \code{'M2'}, then the default value is \code{10}. Otherwise, the value must be \code{NULL}. It works with \code{M2CutoffQualityScore}.
#' @param baseNumPerRow It defines maximum base pairs in each row. The default value is \code{100}.
#' @param heightPerRow It defines the height of each row in chromatogram. The default value is \code{200}.
#' @param 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 \code{0.33}.
#' @param showTrimmed The logical value storing whether to show trimmed base pairs in chromatogram. The default value is \code{TRUE}.
#'
#' @title SangerRead
#' @name SangerRead
#' @export
#'
#' @return A SangerRead instance.
#'
#' @author 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)
SangerRead <- function(printLevel = "SangerRead",
inputSource = "ABIF",
readFeature = "",
readFileName = "",
fastaReadName = NULL,
geneticCode = GENETIC_CODE,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0001,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL,
baseNumPerRow = 100,
heightPerRow = 200,
signalRatioCutoff = 0.33,
showTrimmed = TRUE) {
newRead <- new("SangerRead",
printLevel = printLevel,
inputSource = inputSource,
readFeature = readFeature,
readFileName = readFileName,
fastaReadName = fastaReadName,
geneticCode = geneticCode,
TrimmingMethod = TrimmingMethod,
M1TrimmingCutoff = M1TrimmingCutoff,
M2CutoffQualityScore = M2CutoffQualityScore,
M2SlidingWindowSize = M2SlidingWindowSize,
baseNumPerRow = baseNumPerRow,
heightPerRow = heightPerRow,
signalRatioCutoff = signalRatioCutoff,
showTrimmed = showTrimmed)
return(newRead)
}
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