error_no_subject_qc.Rmd

---
title: "No Subject or QC"
author:
- name: Xiaotao Shen (https://www.shenxt.info/)
date: "Created on 2022-02-08 and updated on `r Sys.Date()`"
output:
  html_document:
    df_print: paged
    toc: no
  pdf_document:
    toc: no
vignette: >
  %\VignetteIndexEntry{align_batch}
  %\VignettePackage{masscleaner}
  % \VignetteEngine{knitr::rmarkdown}
  % \usepackage[utf8]{inputenc}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE, echo=FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE,
  message = TRUE,
  out.width = "100%"
)
```

When you use the functions which need specific identification for `Subject` or `QC` samples in `class` of `sample_info`, if there is a error:

```
Error: error: No Subject samples in object, please check and see here:
```

You need to change the column `class` in `sample_info`.

# Step 1: check the class in your sample_info

```{r,eval=TRUE,echo=FALSE,warning=FALSE, R.options="", message=FALSE, cache=TRUE}
load("object_neg")
object <- object_neg
```

```{r,eval=TRUE,warning=FALSE, R.options="", message=FALSE, cache=TRUE}
library(masscleaner)
library(tidyverse)
object@sample_info$class
```

We can see there are no "Subject" in the class, so we need to change the `case` and `control` to `Subject`.

# Step 2: change class

```{r,eval=TRUE,warning=FALSE, R.options="", message=FALSE, cache=TRUE}
object <- 
  object %>% 
  activate_mass_dataset(what = "sample_info") %>% 
  mutate(class = case_when(
    class == "QC" ~ "QC",
    TRUE ~ "Subject"
  ))
```

```{r,eval=TRUE,warning=FALSE, R.options="", message=FALSE, cache=TRUE}
object@sample_info$class
```

# Session information

```{r,eval=TRUE,warning=FALSE, R.options="", message=FALSE, cache=TRUE}
sessionInfo()
```