estimateMasterFdr {synapter} | R Documentation

## Computes FDR for all possible final peptide combinations

### Description

This function takes all possible combination of `pepfiles` of length greater or equal than 2 and computes the number of estimated incorrect peptides, the number of unique peptides, the number of unique protetypic peptides and the false discovery rate after merging for each combination. The best combination has an fdr lower than `masterFdr` and the highest number of unique (proteotypic) peptides.

### Usage

    estimateMasterFdr(pepfiles, fastafile, masterFdr = 0.025, fdr = 0.01,
      proteotypic = TRUE, missedCleavages = 0, IisL = FALSE,
      maxFileComb = length(pepfiles), verbose = interactive())

### Arguments

`pepfiles` | A `list` of `vector` of final peptide filenames.
`fastafile` | A `character` with the fasta filename.
`masterFdr` | A `numeric` indicating the maximum merged false discovery to be allowed.
`fdr` | Peptide FDR level for individual peptide files filtering.
`proteotypic` | Logical. Should number proteotypic peptides be used to choose best combination and plot results or total number of unique peptides.
`missedCleavages` | Number of maximal missed cleavage sites. Default is 0.
`IisL` | If `TRUE` Isoleucin and Leucin are treated as identical. In this case sequences like "ABCI", "ABCL" are removed because they are not unqiue. If `FALSE` (default) "ABCI" and "ABCL" are reported as unique.
`maxFileComb` | A `numeric` to limit the accepted file combinations to reduce computation time. Default is `length(pepfiles)` meaning no limit set.
`verbose` | Should progress messages be printed?

### Details

The false discovery rate for the master (merged) file is calcualted by summing the number of estimated false discoveries for each individual final peptide file (number of unique peptides in that file multiplied by `fdr`) divided by the total number of unique peptides for that specific combination.

The function returns an instance of the class `"MasterFdrResults"`.

### Value

An instance of class `"MasterFdrResults"`. See details above.

### Author(s)

Laurent Gatto

### References

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

### See Also

The `makeMaster` function to combine the peptide data as suggested by `estimateMasterFdr` into one single master peptide file.

The vignette, accessible with `synapterGuide()` illustrates a complete pipeline using `estimateMasterFdr` and `makeMaster`.

[Package synapter version 2.4.1 Index]