Learn R Programming

ShortRead (version 1.30.0)

FASTQ input and manipulation

Description

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.

Copy Link

Version

Version

1.30.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in ShortRead (1.30.0)

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