A sequence file read in with
readSeqFile is summarized by a C
call. This is a base class with slots common to both
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.
the filename processed by
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.
a numeric vector of the number of sequences of a particular length (the length is the position in the vector).
a numeric vector of the count frequencies of sequences (the sequences are in the name attribute).
a numeric value indicating the proportion of sequences that were sampled for hashing.
a data frame of k-mer frequency by position.
an integer indicating the length of k-mers hashed.
a logical indicating whether the sequences were
a logical indicating whether the k-mers were
Vince Buffalo <[email protected]>
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