synergise {synapter} | R Documentation

## Synergise identification and quantitation results

### Description

Performs a complete default analysis on the files defined in `filenames`, creates a complete html report and saves/exports all results as `csv` and `rds` files. See details for a description of the pipeline and `Synapter` for manual execution of individual steps.

### Usage

    synergise(filenames, master = FALSE, object, outputdir,
      outputfile = paste0("synapter_report_", strftime(Sys.time(),
      "%Y%m%d-%H%M%S"), ".html"), fdr = 0.01, fdrMethod = c("BH",
      "Bonferroni", "qval"), fpr = 0.01, peplen = 7, missedCleavages = 0,
      IisL = FALSE, identppm = 20, quantppm = 20, uniquepep = TRUE,
      span = 0.05, grid.ppm.from = 2, grid.ppm.to = 20, grid.ppm.by = 2,
      grid.nsd.from = 0.5, grid.nsd.to = 5, grid.nsd.by = 0.5,
      grid.subset = 1, grid.n = 0, grid.param.sel = c("auto", "model",
      "total", "details"), mergedEMRTs = c("rescue", "copy", "transfer"),
      template = system.file("reports", "synergise1.Rmd", package = "synapter"),
      verbose = interactive())

### Arguments

`filenames` | A named `list` of file names to be load. The names must be `identpeptide`, `quantpeptide`, `quantpep3d` and `fasta` (could be an RDS file created by `link{createUniquePeptideDbRds}`). `identpeptide` can be a `csv` final peptide file (from PLGS) or a saved `"MasterPeptides"` data object as created by `makeMaster` if working with master peptide data. To serialise the `"MasterPeptides"` instance, use the `saveRDS` function, and file extenstion `rds`.
`master` | A `logical` indicating if the identification final peptide files are master (see `makeMaster`) or regular files. Default is `FALSE`.
`object` | An instance of class `Synapter` that will be copied, processed and returned. If `filenames` are also provided, the latter and `object`'s `inputFiles` will be checked for equality.
`outputdir` | A `character` with the full path to an existing directory.
`outputfile` | A `character` with the file name for the report.
`fdr` | Peptide false discovery rate. Default is 0.01.
`fdrMethod` | P-value adjustment method. One of `"BH"` (default) for Benjamini and HochBerg (1995), `"Bonferroni"` for Bonferroni's single-step adjusted p-values for strong control of the FWER and `"qval"` from the `qvalue` package. See `Synapter` for references.
`fpr` | Protein false positive rate. Default is 0.01.
`peplen` | Minimum peptide length. Default is 7.
`missedCleavages` | Number of allowed missed cleavages. Default is 0.
`IisL` | If `TRUE` Isoleucin and Leucin are treated as equal. In this case sequences like "ABCI", "ABCL" are removed because they are not unqiue. If `FALSE` (default) "ABCI" and "ABCL" are reported as unique.
`identppm` | Identification mass tolerance (in ppm). Default is 20.
`quantppm` | Quantitation mass tolerance (in ppm). Default is 20.
`uniquepep` | A `logical` is length 1 indicating if only unique peptides in the identification and quantitation peptides as well as unique tryptic peptides as defined in the fasta file. Default is `TRUE`.
`span` | The loess span parameter. Default is 0.05.
`grid.ppm.from` | Mass tolerance (ppm) grid starting value. Default is 2.
`grid.ppm.to` | Mass tolerance (ppm) grid ending value. Default is 20.
`grid.ppm.by` | Mass tolerance (ppm) grid step value. Default is 2.
`grid.nsd.from` | Number of retention time stdev grid starting value. Default is 0.5.
`grid.nsd.to` | Number of retention time stdev grid ending value. Default is 5.
`grid.nsd.by` | Number of retention time stdev grid step value. Default is 0.5.
`grid.subset` | Percentage of features to be used for the grid search. Default is 1.
`grid.n` | Absolute number of features to be used for the grid search. Default is 0, i.e ignored.
`grid.param.sel` | Grid parameter selection method. One of `auto` (default), `details`, `model` or `total`. See `Synapter` for details on these selection methods.
`mergedEMRTs` | One of `"rescue"` (default), `"copy"` or `"transfer"`. See the documentation for the `findEMRTs` function in `Synapter` for details.
`template` | A `character` full path to Rmd template.
`verbose` | A `logical` indicating if progress output should be printed to the console. Default is `TRUE`.

### Details

Data can be input as a `Synapter` object if available or as a list of files (see `filenames`) that will be used to read the data in. The html report and result files will be created in the `outputdir` folder. All other input parameters have default values.

The data processing and analysis pipeline is as follows:

1. If `uniquepep` is set to TRUE (default), only unique proteotypic identification and quantitation peptides are retained.

2. Peptides are filtered for a FDR <= `fdr` (default is 0.01) using the "BH" method (see `fdr` and `fdrMethod` parameters for details).

3. Peptide with a mass tolerance > 20 ppms (see `quantppm` and `identppm`) are filtered out.

4. Peptides with a protein false positive rate (as reported by the PLGS software) > `fpr` are filtered out.

5. Common identification and quantitation peptides are merged and a retention time model is created using the Local Polynomial Regression Fitting (`loess` function for the `stats` package) using a default `span` value of 0.05.

6. A grid search to optimise the width in retention time and mass tolerance for EMRTs matching is performed. The default grid search space is from 0.5 to 5 by 0.5 retention time model standard deviations (see `grid.nsd.from`, `grid.nsd.to` and `grid.nsd.by` parameters) and from 2 to 20 by 2 parts per million (ppm) for mass tolerance (see `grid.ppm.from`, `grid.ppm.to` and `grid.ppm.by` parameters). The data can be subset using using an absolute number of features (see `grid.n`) or a fixed percentage (see `grid.subset`). The pair of optimal `nsd` and `ppm` is chosen (see `grid.param.sel` parameter).

7. The quantitation EMRTs are matched using the optimised parameters.

If a master identification file is used (`master` is set to `TRUE`, default is `FALSE`), the relevant actions that have already been executed when the file was created with `makeMaster` are not repeated here.

### Value

Invisibly returns an object of class `Synapter`. Used for its side effect of creating an html report of the run in `outputdir`.

### Author(s)

Laurent Gatto, Sebastian Gibb

### References

Bond N. J., Shliaha P.V., Lilley K.S. and Gatto L. (2013) J. Prot. Research.

### Examples

    output <- tempdir() ## a temporary directory
    synapterTinyData()
    synergise(object = synapterTiny, outputdir = output, outputfile = "synapter.html",
              grid.subset = 0.2)
    htmlReport <- paste0("file:///", file.path(output, "synapter.html")) ## the result report
    ## Not run:
    browseURL(htmlReport) ## open the report with default browser

    ## End(Not run)

[Package synapter version 2.4.1 Index]