---
title: "quality_control"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{quality_control}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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


```{r setup}
library(omiprep)

# import data 
m <- read_metabolon(system.file("extdata", "metabolon_v1.1_example.xlsx", package = "omiprep"), 
                    sheet = "OrigScale",      ## The name of the sheet in the excel file to read in
                    return_Omiprep = TRUE  ## Whether to return a Omiprep object (TRUE) or a list (FALSE)
                    )
```

### Run the quality control pipeline

```{r example}
# run QC
m <- quality_control(m, 
                     source_layer = "input", 
                     sample_missingness  = 0.2, 
                     feature_missingness = 0.2, 
                     feature_skewness_threshold = NULL,
                     feature_skewness_direction = "left",
                     total_sum_abundance_sd  = 5, 
                     outlier_udist       = 5, 
                     outlier_treatment   = "leave_be", 
                     winsorize_quantile  = 1.0, 
                     tree_cut_height     = 0.5, 
                     pc_outlier_sd       = 5, 
                     sample_ids          = NULL, 
                     feature_ids         = NULL, 
                     cores               = 1)
```


### View a summary of the Omiprep object

```{r summary}
# view summary
summary(m)
```