04c-refGMM-labeling.Rmd

---
title: "Creating annotated FCS files"
author:
- name: T.R. Mocking
output:
  BiocStyle::html_document
vignette: |
  %\VignetteIndexEntry{Vignette Title}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r}
RBM18_path <- "<ENTER PATH>"
RBM18_FCS_path <- "<ENTER PATH>"
RBM18_GMMref_label_path <- "<ENTER PATH>"
RBM18_annotated_path <- "<ENTER PATH>"
```

# RBM18

```{r}
df <- read.csv(paste0(RBM18_path, "sample_info.csv"))

for (sample_id in df$RBM18_ID){
  print(sample_id)
  ff <- flowCore::read.FCS(paste0(RBM18_FCS_path, sample_id, ".fcs"), truncate_max_range = FALSE)
  labels <- read.csv(paste0(RBM18_GMMref_label_path, sample_id, ".csv"))
  ff@exprs <- ff@exprs[ff@exprs[, "event_ID"] %in% labels$event_ID, ]
  for (colname in c("Blast", "GMMclf", "GMMref_manual_component", "GMMref_GMMclf_component")){
    col <- as.matrix(labels[, colname])
    colnames(col) <- colname
    ff <- flowCore::fr_append_cols(ff, col)
  }
  flowCore::write.FCS(ff, paste0(RBM18_annotated_path, sample_id, ".fcs"))
}
```

```{r sessionInfo, echo=FALSE}
sessionInfo()
```