Man pages for ShortRead
FASTQ input and manipulation

accessors(Legacy) Accessors for ShortRead classes
AlignedDataFrame(Legacy) AlignedDataFrame constructor
AlignedDataFrame-class(Legacy) "AlignedDataFrame" representing alignment...
AlignedRead(Legacy) Construct objects of class "AlignedRead"
AlignedRead-class(Legacy) "AlignedRead" class for aligned short reads
alphabetByCycleSummarize nucleotide, amino acid, or quality scores by cycle
alphabetScoreEfficiently calculate the sum of quality scores across bases
BowtieQA-class(Legacy) Quality assessment summaries from Bowtie files
cleanRemove sequences with ambiguous nucleotides from short read...
countLinesCount lines in all (text) files in a directory whose file...
deprecatedDeprecated and defunct functions
dotQA-classVirtual class for representing quality assessment results
dustyScoreSummarize low-complexity sequences
ExperimentPath-class(Legacy) "ExperimentPath" class representing a file hierarchy...
FastqQA-classQuality assessment of fastq files and ShortReadQ objects
filterFastqFilter fastq from one file to another
Intensity-class(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure"...
MAQMapQA-class(Legacy) Quality assessment summaries from MAQ map files
polynUtilities for common, simple operations
qaPerform quality assessment on short reads
qa2(Updated) quality assessment reports on short reads
QA-class(Updated) classes for representing quality assessment results
QualityScoreConstruct objects indicating read or alignment quality
QualityScore-classQuality scores for short reads and their alignments
readAligned(Legacy) Read aligned reads and their quality scores into R...
readBaseQuality(Legacy) Read short reads and their quality scores into R...
readBfaToc(Legacy) Get a list of the sequences in a Maq .bfa file
readFastaRead and write FASTA files to or from ShortRead objects
readFastqRead and write FASTQ-formatted files
readIntensities(Legacy) Read Illumina image intensity files
readPrb(Legacy) Read Solexa prb files as fastq-style quality scores
readQseq(Legacy) Read Solexa qseq files as fastq-style quality scores
readXStringColumnsRead one or more columns into XStringSet (e.g., DNAStringSet)...
renewRenew (update) a ShortRead object with new values
reportSummarize quality assessment results into a report
RochePath-class(Legacy) "RochePath" class representing a Roche (454)...
RocheSet-class(Legacy) Roche (454) experiment-wide data container
RtaIntensity(Legacy) Construct objects of class "RtaIntensity"
RtaIntensity-class(Legacy) Class "RtaIntensity"
Sampler-classSampling and streaming records from fastq files
ShortRead-class"ShortRead" class for short reads
ShortRead-deprecatedDeprecated functions from the ShortRead package
ShortRead-packageFASTQ input and manipulation.
ShortReadQ-class"ShortReadQ" class for short reads and their quality scores
Snapshot-classClass '"Snapshot"'
SnapshotFunction-classClass "SnapshotFunction"
SolexaExportQA-class(Legacy) Quality assessment summaries from Solexa export and...
SolexaIntensity(Legacy) Construct objects of class "SolexaIntensity" and...
SolexaIntensity-classClasses "SolexaIntensity" and "SolexaIntensityInfo"
SolexaPath-class(Legacy) "SolexaPath" class representing a standard output...
SolexaSet-class(Legacy) "SolexaSet" coordinating Solexa output locations...
SpTrellis-classClass "SpTrellis"
spViewPerFeatureTools to visualize genomic data
srdistanceEdit distances between reads and a small number of short...
srduplicatedOrder, sort, and find duplicates in XStringSet objects
srFilterFunctions for user-created and built-in ShortRead filters
SRFilter-class"SRFilter" for representing functions operating on ShortRead...
SRFilterResult-class"SRFilterResult" for SRFilter output and statistics
SRSet-class(Legacy) A base class for Roche experiment-wide data
SRUtil-class".SRUtil" and related classes
tablesSummarize XStringSet read frequencies
trimTailsTrim ends of reads based on nucleotides or qualities
ShortRead documentation built on Nov. 1, 2018, 2:08 a.m.