# Analysis of nucleotide, sequence and quality content on fastq files

## Documentation for package ‘seqTools’ version 1.12.0

- 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"'