Nothing
knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(minSNPs) library(BiocParallel) # optional, but needed for parallel processing
read_fasta
is provided as a way to read fasta file, equivalent function, e.g.,
from Biostrings
and read.fasta
from seqinr
can be used.
isolates_from_default <- read_fasta( system.file("extdata", "Chlamydia_mapped.fasta", package = "minSNPs")) processed_from_default <- process_allele(isolates_from_default)
Subsequent analyses can use output from process_allele
.
high_d_snps <- find_optimised_snps(seqc = processed_from_default, metric = "simpson", number_of_result = 1, max_depth = 1, included_positions = c(), excluded_positions = c())
discriminating_snps <- find_optimised_snps(seqc = processed_from_default, metric = "percent", number_of_result = 1, max_depth = 1, included_positions = c(), excluded_positions = c(), goi = c("A_D213", "H_S1432"))
cat("High D SNPs\n") output_result(high_d_snps) cat("SNPws discriminating against A_D213, H_S1432\n") output_result(discriminating_snps)
output_result(high_d_snps, view = "csv", file_name = "high_d_snps.csv") output_result(discriminating_snps, view = "csv", file_name = "discriminating_snps.csv")
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