Analysis of nucleotide, sequence and quality content on fastq files

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Documentation for package ‘seqTools’ version 1.38.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A C F G K M N P R S T W misc

seqTools-package

SeqTools: Bioconductor package for analysis of FASTQ and fasta files.

-- A --

ascii2char

ascii2char: Converting ASCII encoded values to character values.

-- C --

cbDistMatrix	cbDistMatrix function: Calculates pairwise distance matrix from DNA k-mer counts based on a modified Canberra distance.
cbDistMatrix-method	cbDistMatrix function: Calculates pairwise distance matrix from DNA k-mer counts based on a modified Canberra distance.
cbDistMatrix-methods	cbDistMatrix function: Calculates pairwise distance matrix from DNA k-mer counts based on a modified Canberra distance.
char2ascii	ascii2char: Converting ASCII encoded values to character values.
collectDur	collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files.
collectDur-method	collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files.
collectDur-methods	collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files.
collectTime	collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files.
collectTime-method	collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files.
collectTime-methods	collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files.
countDnaKmers	countDnaKmers: Counting k-mers in DNA sequence.
countFastaKmers	countFastaKmers function: Counts DNA k-mers from (compressed) fasta files.
countGenomeKmers	countGenomeKmers: Counting K-mers in DNA sequences.
countSpliceKmers	countSpliceKmers: Counting K-mers on donor (5', upstream) sides (exonic) of splice sites.

-- F --

fastqKmerLocs	fastqKmerLocs function: Counts DNA k-mers position wise from FASTQ files.
fastqKmerSubsetLocs	fastqKmerSubsetLocs function: Counts for a given DNA k-mer subset position wise from FASTQ files.
fastqq	fastqq function: Reading summarizing information from FASTQ files.
Fastqq-class	Class '"Fastqq"'
fileNames	Class '"Fastqq"'
fileNames-method	Class '"Fastqq"'
fileNames-methods	Class '"Fastqq"'

-- G --

gcContent	Class '"Fastqq"'
gcContent-method	Class '"Fastqq"'
gcContent-methods	Class '"Fastqq"'
gcContentMatrix	gcContentMatrix: Returns matrix with read counts for GC content.
gcContentMatrix-method	gcContentMatrix: Returns matrix with read counts for GC content.
gcContentMatrix-methods	gcContentMatrix: Returns matrix with read counts for GC content.
getGCcontent	gcContentMatrix: Returns matrix with read counts for GC content.
getGCcontent-method	gcContentMatrix: Returns matrix with read counts for GC content.
getGCcontent-methods	gcContentMatrix: Returns matrix with read counts for GC content.
getK	Class '"Fastqq"'
getK-method	Class '"Fastqq"'
getK-methods	Class '"Fastqq"'

-- K --

kmerCount	Class '"Fastqq"'
kmerCount-method	Class '"Fastqq"'
kmerCount-methods	Class '"Fastqq"'
kMerIndex	kMerIndex function: Returns array index for given DNA k-mers.

-- M --

maxSeqLen	Class '"Fastqq"'
maxSeqLen-method	Class '"Fastqq"'
maxSeqLen-methods	Class '"Fastqq"'
meltDownK	meltDownK: Condensing DNA k-mer count data to lower k-value (i.e. shorter DNA motifs).
meltDownK-method	meltDownK: Condensing DNA k-mer count data to lower k-value (i.e. shorter DNA motifs).
meltDownK-methods	meltDownK: Condensing DNA k-mer count data to lower k-value (i.e. shorter DNA motifs).
mergedPhred	mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects.
mergedPhred-method	mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects.
mergedPhred-methods	mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects.
mergedPhredQuantiles	mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects.
mergedPhredQuantiles-method	mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects.
mergedPhredQuantiles-methods	mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects.
mergeFastqq	mergeFastqq: Merges two Fastqq object into one.
mergeFastqq-method	mergeFastqq: Merges two Fastqq object into one.
mergeFastqq-methods	mergeFastqq: Merges two Fastqq object into one.

-- N --

nFiles	Class '"Fastqq"'
nFiles-method	Class '"Fastqq"'
nFiles-methods	Class '"Fastqq"'
nNnucs	Class '"Fastqq"'
nNnucs-method	Class '"Fastqq"'
nNnucs-methods	Class '"Fastqq"'
nReads	Class '"Fastqq"'
nReads-method	Class '"Fastqq"'
nReads-methods	Class '"Fastqq"'
nucFreq	Class '"Fastqq"'
nucFreq-method	Class '"Fastqq"'
nucFreq-methods	Class '"Fastqq"'

-- P --

phred	Class '"Fastqq"'
phred-method	Class '"Fastqq"'
phred-methods	Class '"Fastqq"'
phredDist	phredDist: Global relative content of Phred values in Fastqq objects (or subsets).
phredDist-method	phredDist: Global relative content of Phred values in Fastqq objects (or subsets).
phredDist-methods	phredDist: Global relative content of Phred values in Fastqq objects (or subsets).
phredQuantiles	Class '"Fastqq"'
phredQuantiles-method	Class '"Fastqq"'
phredQuantiles-methods	Class '"Fastqq"'
phredTable	phredTable: Returns a data.frame with phred encodings.
plotGCcontent	plotGCcontent: Plots the proportions of relative GC content for all FASTQ files.
plotGCcontent-method	plotGCcontent: Plots the proportions of relative GC content for all FASTQ files.
plotGCcontent-methods	plotGCcontent: Plots the proportions of relative GC content for all FASTQ files.
plotKmerCount	plotKmerCount: Creation of plots DNA for k-mer counts from Fastqq objects.
plotKmerCount-method	plotKmerCount: Creation of plots DNA for k-mer counts from Fastqq objects.
plotKmerCount-methods	plotKmerCount: Creation of plots DNA for k-mer counts from Fastqq objects.
plotMergedPhredQuant	mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects.
plotMergedPhredQuant-method	mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects.
plotMergedPhredQuant-methods	mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects.
plotNucCount	plotNucCount: Plots nucleotide counts from Fastqq objects.
plotNucCount-method	plotNucCount: Plots nucleotide counts from Fastqq objects.
plotNucCount-methods	plotNucCount: Plots nucleotide counts from Fastqq objects.
plotNucFreq	plotNucFreq: Plots the position wise relative nucleotide content for nucleotides 'A','C','G','T'.
plotNucFreq-method	plotNucFreq: Plots the position wise relative nucleotide content for nucleotides 'A','C','G','T'.
plotNucFreq-methods	plotNucFreq: Plots the position wise relative nucleotide content for nucleotides 'A','C','G','T'.
plotPhredDist	phredDist: Global relative content of Phred values in Fastqq objects (or subsets).
plotPhredDist-method	phredDist: Global relative content of Phred values in Fastqq objects (or subsets).
plotPhredDist-methods	phredDist: Global relative content of Phred values in Fastqq objects (or subsets).
plotPhredQuant	plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75% and 90 % quantiles of phred values.
plotPhredQuant-method	plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75% and 90 % quantiles of phred values.
plotPhredQuant-methods	plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75% and 90 % quantiles of phred values.
probeLabel	Class '"Fastqq"'
probeLabel-method	Class '"Fastqq"'
probeLabel-methods	Class '"Fastqq"'
probeLabel<-	Class '"Fastqq"'
probeLabel<--method	Class '"Fastqq"'
probeLabel<--methods	Class '"Fastqq"'
propPhred	propPhred: Lane specific proportion of reads in a specified Phred-region.
propPhred-method	propPhred: Lane specific proportion of reads in a specified Phred-region.
propPhred-methods	propPhred: Lane specific proportion of reads in a specified Phred-region.

-- R --

revCountDnaKmers

revCountDnaKmers: Counting K-mers in DNA sequence.

-- S --

seqLen	Class '"Fastqq"'
seqLen-method	Class '"Fastqq"'
seqLen-methods	Class '"Fastqq"'
seqLenCount	Class '"Fastqq"'
seqLenCount-method	Class '"Fastqq"'
seqLenCount-methods	Class '"Fastqq"'
seqTools	SeqTools: Bioconductor package for analysis of FASTQ and fasta files.
simFastqqRunTimes	simFastqqRunTimes: For given values of k and nSeq the function creates FASTQ files with simulated data, collects k-mer data with the fastqq function and reports the run times for the data collection.
sim_fq	sim_fq: Performs an experimental series of separation capabilities of hierarchical clustering (HC) based on DNA k-mers in FASTQ files using simulated DNA content.

-- T --

trimFastq

trimFastq: Performs sequence removal, trimming (fixed and quality based) and nucleotide masking on FASTQ files.

-- W --

writeFai	writeFai: Create FASTA index file.
writeSimContFastq	writeSimContFastq: Create FASTQ files with simulated k-mer sequences
writeSimFastq	writeSimFastq: Create FASTQ files with simulated DNA k-mer sequences

-- misc --

[-method	Class '"Fastqq"'
[-methods	Class '"Fastqq"'