ShortRead v1.30.0

FASTQ input and manipulation

This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

Functions in ShortRead

Name Description
MAQMapQA-class (Legacy) Quality assessment summaries from MAQ map files
QualityScore Construct objects indicating read or alignment quality
SRUtil-class ".SRUtil" and related classes
SRSet-class (Legacy) A base class for Roche experiment-wide data
ShortReadQA-class Quality assessment of fastq files and ShortReadQ objects
ExperimentPath-class (Legacy) "ExperimentPath" class representing a file hierarchy of data files
Intensity-class (Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities
alphabetByCycle Summarize nucleotide, amino acid, or quality scores by cycle
ShortRead-deprecated Deprecated functions from the ShortRead package
SRFilterResult-class "SRFilterResult" for SRFilter output and statistics
.QA-class Virtual class for representing quality assessment results
SolexaIntensity-class Classes "SolexaIntensity" and "SolexaIntensityInfo"
QualityScore-class Quality scores for short reads and their alignments
ShortRead-class "ShortRead" class for short reads
readAligned (Legacy) Read aligned reads and their quality scores into R representations
renewable Renew (update) a ShortRead object with new values
Snapshot-class Class "Snapshot"
accessors (Legacy) Accessors for ShortRead classes
SolexaSet-class (Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations
readQseq (Legacy) Read Solexa qseq files as fastq-style quality scores
ShortReadQ-class "ShortReadQ" class for short reads and their quality scores
ShortReadBase-package FASTQ input and manipulation.
readBaseQuality (Legacy) Read short reads and their quality scores into R representations
clean Remove sequences with ambiguous nucleotides from short read classes
tables Summarize XStringSet read frequencies
readPrb (Legacy) Read Solexa prb files as fastq-style quality scores
readBfaToc (Legacy) Get a list of the sequences in a Maq .bfa file
AlignedRead-class (Legacy) "AlignedRead" class for aligned short reads
RtaIntensity (Legacy) Construct objects of class "RtaIntensity"
qa Perform quality assessment on short reads
alphabetScore Efficiently calculate the sum of quality scores across bases
deprecated Deprecated and defunct functions
report Summarize quality assessment results into a report
srFilter Functions for user-created and built-in ShortRead filters
BowtieQA-class (Legacy) Quality assessment summaries from Bowtie files
RtaIntensity-class (Legacy) Class "RtaIntensity"
AlignedDataFrame-class (Legacy) "AlignedDataFrame" representing alignment annotations as a data frame
QA-class (Updated) classes for representing quality assessment results
RocheSet-class (Legacy) Roche (454) experiment-wide data container
SolexaExportQA-class (Legacy) Quality assessment summaries from Solexa export and realign files
dustyScore Summarize low-complexity sequences
SnapshotFunction-class Class "SnapshotFunction"
readFastq Read and write FASTQ-formatted files
srdistance Edit distances between reads and a small number of short references
trimTails Trim ends of reads based on nucleotides or qualities
readFasta Read and write FASTA files to or from ShortRead objects
AlignedDataFrame (Legacy) AlignedDataFrame constructor
AlignedRead (Legacy) Construct objects of class "AlignedRead"
SpTrellis-class Class "SpTrellis"
spViewPerFeature Tools to visualize genomic data
qa2 (Updated) quality assessment reports on short reads
readXStringColumns Read one or more columns into XStringSet (e.g., DNAStringSet) objects
countLines Count lines in all (text) files in a directory whose file name matches a pattern
filterFastq Filter fastq from one file to another
Utilites Utilities for common, simple operations
srduplicated Order, sort, and find duplicates in XStringSet objects
SRFilter-class "SRFilter" for representing functions operating on ShortRead objects
SolexaIntensity (Legacy) Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo"
SolexaPath-class (Legacy) "SolexaPath" class representing a standard output file hierarchy
FastqFile-class Sampling and streaming records from fastq files
readIntensities (Legacy) Read Illumina image intensity files
RochePath-class (Legacy) "RochePath" class representing a Roche (454) experiment location
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