Description Usage Arguments Value Author(s) See Also Examples
This function takes a sequence, a vector of randomly sampled sequences, and a
alignment function as input and computes an pairwise alignment score distribution from the input sequence
and all random sequences stored in sampled_strings
.
1 | randSeqDistr(seq, subject, sampled_strings, FUN, ..., comp_cores = 1)
|
seq |
a character vector storing a sequence as string for which random sequences shall be computed. |
subject |
a character vector storing a subject sequence as string to which |
sampled_strings |
an vector object returned by the |
FUN |
a pairwise alignment function such as |
... |
additional arguments that shall be passed to |
comp_cores |
a numeric value specifying the number of cores you want to use for multicore processing. |
a numeric vector storing pairwise alignment scores.
Hajk-Georg Drost
1 2 3 4 5 6 7 8 9 10 11 | # pairwise alignments using Biostrings::pairwiseAlignment() function
# you can also specify the comp_cores argument in case you
# are working with a multicore machine
seq_example <- "MEDQVGFGF"
subject_example <- "AYAIDPTPAF"
randScores <- randSeqDistr(seq_example,subject_example,
randomSeqs(seq_example,10),
Biostrings::pairwiseAlignment,
scoreOnly = TRUE,
comp_cores = 1)
|
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