## ----include = FALSE----------------------------------------------------------
library(rchime)
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## -----------------------------------------------------------------------------
fasta_data <- readRDS(rchime_example("miseq_fasta.rds"))
abundance_data <- readRDS(rchime_example("miseq_abundance.rds"))

strollur <- strollur::new_dataset("rchime de novo example")

strollur::add(strollur, table = fasta_data, type = "sequence")
strollur::assign(strollur, table = abundance_data, type = "sequence_abundance")

strollur

## -----------------------------------------------------------------------------
df <- readRDS(rchime_example("miseq_data_frame_by_sample.rds"))

str(df)

## -----------------------------------------------------------------------------
rchime(strollur)
strollur

data <- rchime(df)
data

## -----------------------------------------------------------------------------
chimera_report <- strollur::report(data, type = "chimera_report")

chimera_report[chimera_report$Chimeric_Status == "Y", ] |> head(n = 5)