SangerAlignment: SangerAlignment

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

Description

the wrapper function for SangerAlignment

Usage

SangerAlignment(inputSource = "ABIF", fastaFileName = "",
  namesConversionCSV = NULL, parentDirectory = "",
  suffixForwardRegExp = "_F.ab1", suffixReverseRegExp = "_R.ab1",
  TrimmingMethod = "M1", M1TrimmingCutoff = 1e-04,
  M2CutoffQualityScore = NULL, M2SlidingWindowSize = NULL,
  baseNumPerRow = 100, heightPerRow = 200, signalRatioCutoff = 0.33,
  showTrimmed = TRUE, refAminoAcidSeq = "", minReadsNum = 2,
  minReadLength = 20, minFractionCall = 0.5, maxFractionLost = 0.5,
  geneticCode = GENETIC_CODE, acceptStopCodons = TRUE,
  readingFrame = 1, minFractionCallSA = 0.5, maxFractionLostSA = 0.5,
  processorsNum = NULL)

Arguments

inputSource	The input source of the raw file. It must be "ABIF" or "FASTA". The default value is "ABIF".
fastaFileName	If inputSource is "FASTA", then this value has to be the name of the FASTA file; if inputSource is "ABIF", then this value is "" by default.
namesConversionCSV	The file path to the CSV file that provides read names that follow the naming regulation. If inputSource is "FASTA", then users need to prepare the csv file or make sure the original names inside FASTA file are valid; if inputSource is "ABIF", then this value is NULL by default.
parentDirectory	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.
suffixForwardRegExp	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 "_F.ab1".
suffixReverseRegExp	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 "_R.ab1".
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.
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 "".
minReadsNum	The minimum number of reads required to make a consensus sequence, must be 2 or more. The default value is 2.
minReadLength	Reads shorter than this will not be included in the readset. The default 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.
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.
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.
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.
acceptStopCodons	The logical value TRUE or FALSE. TRUE (the defualt): keep all reads, regardless of whether they have stop codons; FALSE: reject reads with stop codons. If FALSE is selected, then the number of stop codons is calculated after attempting to correct frameshift mutations (if applicable).
readingFrame	1, 2, or 3. Only used if accept.stop.codons == FALSE. This specifies the reading frame that is used to determine stop codons. If you use a refAminoAcidSeq, then the frame should always be 1, since all reads will be shifted to frame 1 during frameshift correction. Otherwise, you should select the appropriate reading frame.
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.
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.
processorsNum	The number of processors to use, or NULL (the default) for all available processors.

Value

A SangerAlignment instance.

Author(s)

Kuan-Hao Chao

Examples

rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "RBNII")
suffixForwardRegExp <- "_[0-9]*_F.ab1"
suffixReverseRegExp <- "_[0-9]*_R.ab1"
sangerAlignment <- SangerAlignment(
                       inputSource            = "ABIF",
                       parentDirectory       = parentDir,
                       suffixForwardRegExp   = suffixForwardRegExp,
                       suffixReverseRegExp   = suffixReverseRegExp,
                       refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
                       TrimmingMethod        = "M1",
                       M1TrimmingCutoff      = 0.0001,
                       M2CutoffQualityScore  = NULL,
                       M2SlidingWindowSize   = NULL,
                       baseNumPerRow         = 100,
                       heightPerRow          = 200,
                       signalRatioCutoff     = 0.33,
                       showTrimmed           = TRUE,
                       processorsNum         = 2)

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