require(single)
refseq_fasta<- system.file("extdata", "ref_seq.fasta", package = "single")
ref_seq = Biostrings::readDNAStringSet(refseq_fasta)
train_reads_example <- system.file("extdata", "train_seqs_500.sorted.bam",
package = "single")
## Generate fits_example.txt
counts_pnq <- pileup_by_QUAL(bam_file=train_reads_example,
pos_start=1,
pos_end=10)
p_prior_errors <- p_prior_errors(counts_pnq=counts_pnq,
output_file="none",
save=F)
p_prior_mutations <- p_prior_mutations(rates.matrix = mutation_rate,
mean.n.mut = 5,
ref_seq = ref_seq,
save = FALSE,
output_file="none")
fits_example <- fit_logregr(counts_pnq = counts_pnq,
ref_seq=ref_seq,
p_prior_errors = p_prior_errors,
p_prior_mutations = p_prior_mutations,
save=F)
write.table(fits_example, file="single/inst/extdata/fits_example.txt")
## Generate train_example.txt
train_example <- single_train(bamfile=train_reads_example,
refseq_fasta=refseq_fasta,
rates.matrix=mutation_rate,mean.n.mutations=5,
pos_start=1,pos_end=10,)
write.table(train_example, file="single/inst/extdata/train_example.txt")
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