README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# pnnl.diann.utils

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The goal of pnnl.diann.utils is 

  1. A set of functions to analyze DIA-NN outputs and convert them to `MSnSet` objects for downstream analysis with [`MSnSet.utils`](https://github.com/PNNL-Comp-Mass-Spec/MSnSet.utils).
  2. Assembling paths for analyzing files directly from DMS.
  3. (in-progress) General workflow for *plexDIA* analysis. 
  
```{r , echo = FALSE, fig.width = 4, fig.cap = "Overview of `pnnl.diann.utils` package workflow. Package functions are in `monospace`."}
knitr::include_graphics(path = "man/figures/README-/pnnl.diann.utils_workflow_DARK.png")
```

## Installation

You can install the development version of pnnl.diann.utils from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("PNNL-Comp-Mass-Spec/DIANN.utils")
```

## Example datasets

Example gene group (*gg*) and protein group (*pg*) matrices, and precursors (*pq*) report are found in build`inst/extdata/`. 

  - `diann_report.tsv` is example data from [`diann_rpackage`](https://github.com/vdemichev/diann-rpackage)
  - `QC_Mam` matrices are from `\\proto-8\Lumos02\2023_4\QC_Mam_19_01_b_DIA_trap_60min_19Dec23_Pippin_WBEH-23-05-18\DNN202312200344_Auto2255735`



## Converting Protein Groups Matrix to `MSnSet`


```{r example, warning = FALSE, message = FALSE, error = FALSE}
library(pnnl.diann.utils)


pg_matrix_path <- system.file("extdata",
                              "QC_Mam_19_01_b_DIA_report.pg_matrix.tsv",
                              package = "pnnl.diann.utils")


pnnl.diann.utils::pgmatrix_to_msnset(pg_matrix_path)
```
## Assembling file paths from Data Package number

While running DIA-NN from `kaiju` or other PNNL servers, DIA-NN can pull files directly from DMS, saving time and redundancy incurred from copying LC-MS files over with a minimal impact on overall DIA-NN analysis time. To this end an absolute file path needs to be provided to DIA-NN for each LC-MS file. `dms_dataset_path` assembles the paths for all files in a [DMS Data Package](https://prismwiki.pnl.gov/wiki/Data_Package). The function requires [`PNNL>DMS.utils`](https://github.com/PNNL-Comp-Mass-Spec/PNNL.DMS.utils) and access to PNNL network. 

```{r}
paths <-pnnl.diann.utils::dms_dataset_path(
  data_package_num = 5293,
  file_type = ".raw",
  diann_console = TRUE
  )


paths[1:3,]


```

Note the outputs above are already formatted for the  [DIA-NN Console Command](https://github.com/vdemichev/DiaNN?tab=readme-ov-file#command-line-reference). They can then be saved (see below) and pasted into the *Console Commands* box on DIA-NN. Setting `diann_console = FALSE` will return the absolute LC-MS file paths only. 

```{r, eval = FALSE}

write_tsv(x = diann_raw_paths,
          escape = "none",
          col_names = FALSE, 
          file = "DATA/PATH.txt")

```