Generate a Distribution of Alignment Scores Based on Random Sequences

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.

randSeqDistr(seq, subject, sampled_strings, FUN, ..., comp_cores = 1)

Arguments

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 seq shall be pairwise aligned.
sampled_strings	an vector object returned by the randomSeqs function.
FUN	a pairwise alignment function such as pairwiseAlignment or any other function that takes sequence arguments as first and second input.
...	additional arguments that shall be passed to FUN.
comp_cores	a numeric value specifying the number of cores you want to use for multicore processing.

Value

a numeric vector storing pairwise alignment scores.

See also

evalAlignment, randomSeqs

Examples

# 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)