---
title: "Introduction to MultiOmicsSuite"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{intro}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
options(rmarkdown.html_vignette.check_title = FALSE)
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(MOSuite)
library(dplyr)
```

```{r nidap_data}
options(moo_print_plots = TRUE)

moo_nidap <- create_multiOmicDataSet_from_dataframes(
  sample_metadata = as.data.frame(nidap_sample_metadata),
  counts_dat = as.data.frame(nidap_raw_counts)
) |>
  clean_raw_counts() |>
  filter_counts(group_colname = "Group") |>
  normalize_counts(group_colname = "Group") |>
  batch_correct_counts(
    covariates_colname = "Group",
    batch_colname = "Batch",
    label_colname = "Label"
  ) |>
  diff_counts(
    count_type = "filt",
    covariates_colnames = c("Group", "Batch"),
    contrast_colname = c("Group"),
    contrasts = c("B-A", "C-A", "B-C"),
    input_in_log_counts = FALSE,
    return_mean_and_sd = FALSE,
    voom_normalization_method = "quantile",
  ) |>
  filter_diff()

moo_nidap@analyses$diff |>
  join_dfs_wide() |>
  head()

moo_nidap@analyses$diff_filt |> head()
```

## The multiOmicDataSet object structure

```{r str_moo}
str(moo_nidap)
```