SequenceSummary-class: 'SequenceSummary' class representing the summaries of a...

In qrqc: Quick Read Quality Control

Description

A sequence file read in with readSeqFile is summarized by a C call. This is a base class with slots common to both FASTQSummary and FASTASummary. This is not usually instantiated directly.

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

filename

the filename processed by readSeqFile.

base.freqs

a data frame of base frequencies by position. Each column is a nucleotide (there is a column for position too), and each row contains the count frequencies of bases for that position.

seq.lengths

a numeric vector of the number of sequences of a particular length (the length is the position in the vector).

hash

a numeric vector of the count frequencies of sequences (the sequences are in the name attribute).

hash.prop

a numeric value indicating the proportion of sequences that were sampled for hashing.

kmer

a data frame of k-mer frequency by position.

k

an integer indicating the length of k-mers hashed.

hashed

a logical indicating whether the sequences were hashed in readSeqFile.

kmers.hashed

a logical indicating whether the k-mers were hashed in readSeqFile.

Author(s)

Vince Buffalo <[e-mail]>

See Also

FASTQSummary and FASTASummary are the classes that inherit from SequenceSummary.

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

Examples

showClass("SequenceSummary")

qrqc documentation built on Nov. 8, 2020, 7:03 p.m.