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ShortRead

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 (62)

AlignedDataFrame

(Legacy) AlignedDataFrame constructor

AlignedDataFrame-class

(Legacy) "AlignedDataFrame" representing alignment annotations as a data frame

AlignedRead

(Legacy) Construct objects of class "AlignedRead"

AlignedRead-class

(Legacy) "AlignedRead" class for aligned short reads

BowtieQA-class

(Legacy) Quality assessment summaries from Bowtie files

ExperimentPath-class

(Legacy) "ExperimentPath" class representing a file hierarchy of data files

FastqQA-class

Quality assessment of fastq files and ShortReadQ objects

Intensity-class

(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base classes for short read image intensities

MAQMapQA-class

(Legacy) Quality assessment summaries from MAQ map files

QA-class

(Updated) classes for representing quality assessment results

QualityScore

Construct objects indicating read or alignment quality

QualityScore-class

Quality scores for short reads and their alignments

RochePath-class

(Legacy) "RochePath" class representing a Roche (454) experiment location

RocheSet-class

(Legacy) Roche (454) experiment-wide data container

RtaIntensity

(Legacy) Construct objects of class "RtaIntensity"

RtaIntensity-class

(Legacy) Class "RtaIntensity"

SRFilter-class

"SRFilter" for representing functions operating on ShortRead objects

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

Sampler-class

Sampling and streaming records from fastq files

ShortRead-class

"ShortRead" class for short reads

ShortRead-deprecated

Deprecated functions from the ShortRead package

ShortRead-package

FASTQ input and manipulation.

ShortReadQ-class

"ShortReadQ" class for short reads and their quality scores

Snapshot-class

Class "Snapshot"

SnapshotFunction-class

Class "SnapshotFunction"

SolexaExportQA-class

(Legacy) Quality assessment summaries from Solexa export and realign files

SolexaIntensity

(Legacy) Construct objects of class "SolexaIntensity" and "SolexaIntensityInfo"

SolexaIntensity-class

Classes "SolexaIntensity" and "SolexaIntensityInfo"

SolexaPath-class

(Legacy) "SolexaPath" class representing a standard output file hierarchy

SolexaSet-class

(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations

SpTrellis-class

Class "SpTrellis"

accessors

(Legacy) Accessors for ShortRead classes

alphabetByCycle

Summarize nucleotide, amino acid, or quality scores by cycle

alphabetScore

Efficiently calculate the sum of quality scores across bases

clean

Remove sequences with ambiguous nucleotides from short read classes

countLines

Count lines in all (text) files in a directory whose file name matches a pattern

deprecated

Deprecated and defunct functions

dotQA-class

Virtual class for representing quality assessment results

dustyScore

Summarize low-complexity sequences

filterFastq

Filter fastq from one file to another

polyn

Utilities for common, simple operations

Perform quality assessment on short reads

qa2

(Updated) quality assessment reports on short reads

readAligned

(Legacy) Read aligned reads and their quality scores into R representations

readBaseQuality

(Legacy) Read short reads and their quality scores into R representations

readBfaToc

(Legacy) Get a list of the sequences in a Maq .bfa file

readFasta

Read and write FASTA files to or from ShortRead objects

readFastq

Read, write, and count records in 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

readXStringColumns

Read one or more columns into XStringSet (e.g., DNAStringSet) objects

renew

Renew (update) a ShortRead object with new values

report

Summarize quality assessment results into a report

spViewPerFeature

Tools to visualize genomic data

srFilter

Functions for user-created and built-in ShortRead filters

srdistance

Edit distances between reads and a small number of short references

srduplicated

Order, sort, and find duplicates in XStringSet objects

tables

Summarize XStringSet read frequencies

trimTails

Trim ends of reads based on nucleotides or qualities

ShortRead

FASTQ input and manipulation

v1.48.0

Artistic-2.0

Authors

Martin Morgan, Michael Lawrence, Simon Anders

Initial release

ShortRead

Functions (62)

ShortRead

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