alphabetByCycle: Summarize nucleotide, amino acid, or quality scores by cycle

Description

alphabetByCycle summarizes nucleotides, amino acid, or qualities by cycle, e.g., returning the number of occurrences of each nucleotide A, T, G, C across all reads from 36 cycles of a Solexa lane.

Usage

alphabetByCycle(stringSet, alphabet, ...)

Arguments

stringSet

A R object representing the collection of reads, amino acid sequences, or quality scores, to be summarized.

alphabet

The alphabet (character vector of length 1 strings) from which the sequences in stringSet are composed. Methods often define an appropriate alphabet, so that the user does not have to provide one.

...

Additional arguments, perhaps used by methods defined on this generic.

Value

A matrix with number of rows equal to the length of alphabet and columns equal to the maximum width of reads or quality scores in the string set. Entries in the matrix are the number of times, over all reads of the set, that the corresponding letter of the alphabet (row) appeared at the specified cycle (column).

Details

The default method requires that stringSet extends the XStringSet class of Biostrings.

The following method is defined, in addition to methods described in class-specific documentation:

alphabetByCycle

signature(stringSet = "BStringSet"): this method uses an alphabet spanning all ASCII characters, codes 1:255.

Examples

Run this code

showMethods("alphabetByCycle")

sp <- SolexaPath(system.file('extdata', package='ShortRead'))
rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt")
alphabetByCycle(sread(rfq))

abcq <- alphabetByCycle(quality(rfq))
dim(abcq)
## 'high' scores, first and last cycles
abcq[64:94,c(1:5, 32:36)]