## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE---------------- ## For links library("BiocStyle") ## Bib setup library("RefManageR") ## Write bibliography information bib <- c( R = citation(), BiocStyle = citation("BiocStyle")[1], data.table = citation("data.table")[1], stringr = citation("stringr")[1] ) ## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", error = FALSE, warning = FALSE, message = FALSE, crop = NULL ) ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("lineagespot") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() ## ----setup-------------------------------------------------------------------- library(lineagespot) ## ----eval=TRUE---------------------------------------------------------------- results <- lineagespot(vcf_folder = system.file("extdata", "vcf-files", package = "lineagespot"), gff3_path = system.file("extdata", "NC_045512.2_annot.gff3", package = "lineagespot"), ref_folder = system.file("extdata", "ref", package = "lineagespot")) ## ----------------------------------------------------------------------------- # overall table head(results$variants.table) ## ----------------------------------------------------------------------------- # lineages' hits head(results$lineage.hits) ## ----------------------------------------------------------------------------- # lineagespot report head(results$lineage.report) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()