## ----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)

## -----------------------------------------------------------------------------
strollur_results <- rchime(strollur)

strollur

data_frame_results <- rchime(df)

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

## -----------------------------------------------------------------------------
strollur_results$chimeras |> head(n = 10)

## -----------------------------------------------------------------------------
names(data_frame_results$set_abundance_values)

data_frame_results$set_abundance_values$samples

sequences_names <- c(
  "M00967_43_000000000-A3JHG_1_1103_5171_14027",
  "M00967_43_000000000-A3JHG_1_1101_10133_8460"
)

df[df$sequence_name %in% sequences_names, c(1, 3, 4)]

data_frame_results$set_abundance_values$sequence_name[1:2]

data_frame_results$set_abundance_values$abundance[1:2]

## -----------------------------------------------------------------------------
df[
  df$sequence_name %in% "M00967_43_000000000-A3JHG_1_1103_5171_14027",
  c(1, 3, 4)
]

data_frame_results$set_abundance_values$samples

data_frame_results$set_abundance_values$abundance[
  data_frame_results$set_abundance_values$sequence_name %in%
    "M00967_43_000000000-A3JHG_1_1103_5171_14027"
]