FASTASummary-class: 'FASTASummary' class representing the summaries of a FASTA...
In qrqc: Quick Read Quality Control

Description Slots Author(s) See Also Examples

This class contains the same slots as the SequenceSummary, but it is used to indicate the data originated from a FASTA file.

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.

FASTASummary has the slots inherited from SequenceSummary.

Vince Buffalo <vsbuffalo@ucdavis.edu>

FASTQSummary is the counterpart of this class for FASTQ data.

readSeqFile is the function that takes a FASTA file and returns a FASTASummary object.

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

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