FASTQSummary-class: 'FASTQSummary' class representing the summaries of a FASTQ...

Description Slots Author(s) See Also Examples

Description

This class contains the same slots as the SequenceSummary, as well as additional slots for quality information.

Note that many accessor functions transform data in the slots into data frames. The data in the slots is mostly untransformed and less easy to work with directly, so using the accessor functions is recommended.

Slots

In addition to the slots inherited from SequenceSummary, FASTQSummary contains:

quality

a string indicating the type of quality (used to convert ASCII characters to quality integers). Either "phred", "solexa", or "illumina".

qual.freqs

a data frame of quality frequencies by position, if the file was a FASTQ file.

mean.qual

a numeric that is the mean quality across all positions, weighted by the number of reads that extended to that position.

Author(s)

Vince Buffalo <[email protected]>

See Also

FASTASummary is the counterpart of this class for FASTA data.

readSeqFile is the function that takes a FASTQ file and returns a FASTQSummary object.

basePlot is a function that plots the distribution of bases over sequence length for a particular FASTQSummary object. gcPlot combines and plots the GC proportion.

qualPlot is a function that plots the distribution of qualities over sequence length for a particular FASTQSummary object.

seqlenPlot is a function that plots a histogram of sequence lengths for a particular FASTQSummary object.

kmerKLPlot is a function that uses Kullback-Leibler divergence to make a plot that can aid in finding possible contamination (if readSeqFile had kmer=TRUE).

kmerEntropyPlot is a function that plots the Shannon entropy of k-mers per position.

There are acccessor functions getQual, getBase, getBaseProp, getSeqlen, getKmer, getGC for transforming the raw data in the object's slot (direct from the C call) to more usable data frames.

Examples

1
showClass("FASTQSummary")

qrqc documentation built on Nov. 1, 2018, 2:24 a.m.