35-DIPG_recount2_model.Rmd

---
title: "DIPG: applying MultiPLIER"
output:   
  html_notebook: 
    toc: true
    toc_float: true
---

**J. Taroni 2018**

Apply the MultiPLIER (recount2) model to the two datasets prepped in 
`34-DIPG_data_cleaning`.

## Set up

```{r}
`%>%` <- dplyr::`%>%`
source(file.path("util", "plier_util.R"))
```

Directories for this notebook

```{r}
# plot and result directory setup for this notebook
plot.dir <- file.path("plots", "35")
dir.create(plot.dir, recursive = TRUE, showWarnings = FALSE)
results.dir <- file.path("results", "35")
dir.create(results.dir, recursive = TRUE, showWarnings = FALSE)
```

## Read in data

### recount2 PLIER model

```{r}
recount.file <- file.path("data", "recount2_PLIER_data", 
                          "recount_PLIER_model.RDS")
recount.plier <- readRDS(recount.file)
```

### DIPG Expression data

```{r}
# we want this is matrix form, with the gene symbols as rownames
gse50021 <- readr::read_tsv(file.path("data", "expression_data", 
                                      "GSE50021_mean_agg.pcl")) %>%
  as.data.frame() %>%
  tibble::column_to_rownames("Gene") %>%
  as.matrix()
```

```{r}
e.geod.file <- 
  file.path("data", "expression_data", 
            "DIPG_E-GEOD-26576_hgu133plus2_SCANfast_with_GeneSymbol.pcl")
gse26576 <- readr::read_tsv(e.geod.file) %>%
  dplyr::select(-EntrezID) %>%
  as.data.frame() %>%
  tibble::column_to_rownames("GeneSymbol") %>%
  as.matrix()
```

## Apply the model

### `GSE50021`

```{r}
gse50021.b <- GetNewDataB(exprs.mat = gse50021,
                          plier.model = recount.plier)
```

Save the `B` matrix to file

```{r}
saveRDS(gse50021.b, file = file.path(results.dir, "GSE50021_recount2_B.RDS"))
```

### `E-GEOD-26576`

Now the next expression dataset

```{r}
gse26576.b <- GetNewDataB(exprs.mat = gse26576,
                          plier.model = recount.plier)
```

Save to file

```{r}
saveRDS(gse26576.b, file = file.path(results.dir, 
                                     "E-GEOD-26576_recount2_B.RDS"))
```