synapter ion mobility example

ionmobility.Rmd

# Ion Mobility Example

```{r setup, include=FALSE}
library(knitr)
opts_chunk$set(fig.height=10, fig.width=14, fig.path="figure/ionmobility/", cache=TRUE, autodep=TRUE, tidy=FALSE)
```
## Default Synapter Preprocessing

(same as in `synergise`)

```{r loadsynapter}
suppressPackageStartupMessages(library("synapter"))
```

### File Import
```{r fileimport}
dataPath <- file.path("..", "..", "..", "playground", "data",
                      "biological_replicas_for_synapter")
iaPath <- file.path(dataPath, "HDMSE", "ia")
apexPath <- file.path(dataPath, "HDMSE", "apex")

input <- list(
  identpeptide=file.path(iaPath,
                         "fermentor_02_sample_15_HDMSE_01_20140303114821",
                         "fermentor_02_sample_15_HDMSE_01_IA_final_peptide.csv"),
  quantpeptide=file.path(iaPath,
                         "fermentor_03_sample_15_HDMSE_01_20140303120343",
                         "fermentor_03_sample_15_HDMSE_01_IA_final_peptide.csv"),
  quantpep3d=file.path(apexPath,
                       "fermentor_03_sample_15_HDMSE_01_20140302183822",
                       "fermentor_03_sample_15_HDMSE_01_Pep3DAMRT.csv"),
  fasta=file.path(dataPath,
                  "S.cerevisiae_uniprot_reference_canonical_16_09_13.fasta"))

## only for reproducibility
set.seed(1)
system.time(s <- Synapter(input))
```

### Filtering
```{r filtering}
filterUniqueDbPeptides(s, verbose=TRUE)
fdr <- fpr <- 0.05
ppm <- 20

filterIdentPepScore(s, method="BH", fdr=fdr)
filterQuantPepScore(s, method="BH", fdr=fdr)
filterIdentProtFpr(s, fpr=fpr)
filterQuantProtFpr(s, fpr=fpr)
filterIdentPpmError(s, ppm=ppm)
filterQuantPpmError(s, ppm=ppm)
```

### RT Model and Grid Search
```{r rtmodel}
mergePeptides(s)

modelRt(s, span=0.05)

system.time(searchGrid(s, verbose=FALSE))

setBestGridParams(s)

findEMRTs(s)
s
```

## Ion Mobility

```{r imsummary}
set.seed(1) # only for demonstration
m <- synapter:::.plotIonMobilitySummary(s)
```
```{r imsummarytable, results="asis"}
kable(m[1:25,], row.names=FALSE)
```