Outline of new IDBac functions for programming with IDBac

idbac_programming_outline.rmd

---
title: "Programming IDBac"
author: "Chase Clark"
date: "1/31/2020"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(eval = FALSE, include = TRUE)
```


Things people want to do:

- Create IDBac database
```{r}
idbac_create(fileName = "idbac_experiment",
             filePath = "C:/Users/my/path")[[1]]
```

- Connect to IDBac database
```{r}
idbac_connect(fileName = "idbac_experiment",
              filePath = "C:/Users/my/path")[[1]]
```


Retrieve all sample IDs in the database
```{r}
idbac_available_samples(pool = pool,
                        whetherProtein = FALSE,
                        allSamples = TRUE)
```

Retrieve entire metadata table
```{r}
idbac_get_metadata(pool = pool)
```

Retrieve metadata table by ID
```{r}
idbac_get_metadata(strainID = c("my_strain_1", "my_strain_2"),
                   pool = pool)
```

Retrieve metadata column by ID
```{r}
idbac_get_metadata(strainID = c("my_strain_1", "my_strain_2"),
                   metadataColumn = "speccies",
                   pool = pool)
```



Retreive all spectra from the database by ID
```{r}
idbac_get_spectra(pool = pool,
                  sampleID = sampleID,
                  protein = TRUE,
                  smallmol = FALSE)
```


Collapse all replicates of retrieved spectra

```{r}
MALDIquant::averageMassSpectra(IDBacApp::idbac_get_spectra(pool = pool,
                                                           sampleID = sampleID, 
                                                           protein = TRUE,
                                                           smallmol = FALSE))
```


Retreive all peaks from the database by ID
```{r}
idbac_get_peaks(pool = pool,
                sampleIDs = sampleIDs,
                protein = TRUE)
```


Collapse all replicates of retrieved peaks
```{r}
IDBacApp::collapseReplicates(pool = pool,
                             sampleIDs = sample_ids ,
                             peakPercentPresence = 0.6,
                             lowerMassCutoff = 3000,
                             upperMassCutoff = 15000,
                             minSNR = 10,
                             tolerance = .002,
                             protein = TRUE)
```



Plot mirror plot

```{r}
assembleMirrorPlots(sampleID1 = "sample_id_from_pool_1",
                    sampleID2 = "sample_id_from_pool_2",
                    peakPercentPresence = 0.7,
                    lowerMassCutoff = 3000,
                    upperMassCutoff = 15000,
                    minSNR = 4, 
                    tolerance = 0.002,
                    pool1 = pool1,
                    pool2 = pool2) # pool2 can be the same as pool1
```




Create a protein-data dendrogram
```{r}
idbac_dendrogram_creator(bootstraps = 0 ,
                         distanceMethod = "cosine",
                         clusteringMethod = "average",
                         proteinMatrix = proteinMatrix)
```

Create a metabolite association network

MIA

Create a fuzzy vector matrix

```{r}
createFuzzyVector(massStart = 3000L,
                  massEnd = 15000L,
                  ppm = 500,
                  massList = lapply(peak_data, function(x) x@mass),
                  intensityList = lapply(peak_data, function(x) x@intensity))
```







Check IDBac database version
```{r}
idbac_db_version(pool = pool)
```

Update IDBac database version
```{r}
idbac_update_db(pool = pool)
```