SangerAlignment-class: SangerAlignment

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

Description

An S4 class containing SangerContigs lists and contigs alignment results which corresponds to a final alignment in Sanger sequencing.

Slots

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

If inputSource is "ABIF", then this value is the path of the parent directory storing all reads in ABIF format you wish to analyse and cannot be NULL. In SangerAlignment, all reads in subdirectories will be scanned recursively. If inputSource is "FASTA", then this value is NULL by default.

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".

trimmingMethodSA

The read trimming method for all SangerRead S4 instances in SangerAlignment. The value must be "M1" (the default) or 'M2'. All SangerReads must have the same trimming method.

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.

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.

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 "".

contigList

A list storing all SangerContigs S4 instances.

contigsConsensus

The consensus read of all SangerContig S4 instances in DNAString object.

contigsAlignment

The alignment of all SangerContig S4 instances with the called consensus sequence in DNAStringSet object. Users can use BrowseSeqs() to view the alignment.

contigsTree

A phylo instance returned by bionj function in ape package. It can be used to draw the tree.

Author(s)

Kuan-Hao Chao

Examples

## Input From ABIF file format (Regex)
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, 'Allolobophora_chlorotica', 'ACHLO')
suffixForwardRegExp <- "_[0-9]*_F.ab1"
suffixReverseRegExp <- "_[0-9]*_R.ab1"
sangerAlignment <- new("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)

## Input From ABIF file format (Csv three column)
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
parentDir <- file.path(rawDataDir, 'Allolobophora_chlorotica', 'ACHLO')
namesConversionCSV <- file.path(rawDataDir, "ab1", "SangerAlignment",
"names_conversion.csv")
sangerAlignment <- new("SangerAlignment",
                       inputSource           = "ABIF",
                       parentDirectory       = parentDir,
                       namesConversionCSV    = namesConversionCSV,
                       refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
                       TrimmingMethod        = "M1",
                       M1TrimmingCutoff      = 0.0001,
                       M2CutoffQualityScore  = NULL,
                       M2SlidingWindowSize   = NULL,
                       baseNumPerRow         = 100,
                       heightPerRow          = 200,
                       signalRatioCutoff     = 0.33,
                       showTrimmed           = TRUE,
                       processorsNum         = 2)

## Input From FASTA file format (No Csv - Regex)
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
fastaFN <- file.path(rawDataDir, "fasta",
                     "SangerAlignment", "Sanger_all_reads.fa")
suffixForwardRegExpFa <- "_[0-9]*_F$"
suffixReverseRegExpFa <- "_[0-9]*_R$"
sangerAlignmentFa <- new("SangerAlignment",
                         inputSource           = "FASTA",
                         fastaFileName         = fastaFN,
                         suffixForwardRegExp   = suffixForwardRegExpFa,
                         suffixReverseRegExp   = suffixReverseRegExpFa,
                         refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
                         processorsNum         = 2)

## Input From FASTA file format (Csv three column method)
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
fastaFN <- file.path(rawDataDir, "fasta",
                     "SangerAlignment", "Sanger_all_reads.fa")
namesConversionCSV <- file.path(rawDataDir, "fasta",
                                "SangerAlignment", "names_conversion.csv")
sangerAlignmentFa <- new("SangerAlignment",
                         inputSource           = "FASTA",
                         fastaFileName         = fastaFN,
                         namesConversionCSV    = namesConversionCSV,
                         refAminoAcidSeq = "SRQWLFSTNHKDIGTLYFIFGAWAGMVGTSLSILIRAELGHPGALIGDDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMLGAPDMAFPRMNNMSFWLLPPALSLLLVSSMVENGAGTGWTVYPPLSAGIAHGGASVDLAIFSLHLAGISSILGAVNFITTVINMRSTGISLDRMPLFVWSVVITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAVPTGIKIFSWLATLHGTQLSYSPAILWALGFVFLFTVGGLTGVVLANSSVDIILHDTYYVVAHFHYVLSMGAVFAIMAGFIHWYPLFTGLTLNNKWLKSHFIIMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTTWNIVSTIGSTISLLGILFFFFIIWESLVSQRQVIYPIQLNSSIEWYQNTPPAEHSYSELPLLTN",
                         processorsNum         = 2)

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