sfinx: SFINX (Straightforward Filtering INdeX).
In sfinx: Straightforward Filtering Index for AP-MS Data Analysis (SFINX)

Description Usage Arguments Details Value Examples

sfinx identifies the true-positive protein interactions in affinity purification - mass spectrometry data sets and in similar co-complex interactomics data sets. It is highly accurate, fast and independent of external data input.

It is also available via the Web interface at http://sfinx.ugent.be, which has extra analysis and visualization features.

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sfinx(InputData, BaitVector, BackgroundRatio = 5,
  BackgroundIdentity = "automatic", BaitInfluence = FALSE,
  ConstantLimit = TRUE, FWERType = "B")

`InputData`	A strictly numeric matrix with unique proteins as rownames and unique projects as colnames. The cells of the matrix are filled with the associated peptide counts. Cells that have no associated peptide counts have to be filled with a zero.
`BaitVector`	A character vector with all the bait proteins of interest. These proteins should all be present as the exact same rownames in `InputData`. `sfinx` will control this, and it will report possible deviations.
`BackgroundRatio`	Advanced. A natural number equal or bigger than 2, that specifies the maximal ratio of total considered projects over the amount of bait projects. If this parameter equals for example 5, it will take into account 4 times as much non-bait projects as it uses bait projects. `sfinx` will preferably first select the non-bait projects with most peptide counts as negative controls.
`BackgroundIdentity`	Deprecated. A character string or character vector describing the background projects. `"automatic"` is the advised default entry. However, all extra or alternative entries will be matched to the column headers and taken into account when possible.
`BaitInfluence`	Advanced. A logical. When TRUE, `sfinx` uses only the non-bait negative control projects with the biggest amount of data for the calculation of the background, but no negative control projects associated with other baits in the analysis. When FALSE, `sfinx` uses both.
`ConstantLimit`	Advanced. A logical. When TRUE, an internal cut-off is used that is a simplified constant for the actual complete calculation of the binomial equivalent. This is the version of `sfinx` that was used in the article (Titeca et al., J. Proteome Res., 2016). When FALSE, the complete calculation of the binomial equivalent is done. Some datasets with many highly abundant proteins can benefit from having this parameter FALSE.
`FWERType`	Advanced. A character string that equals `"B"`, `"HolmB"` or `"Sidak"`. `"B"` gives the Bonferroni correction for the family wise error rate (FWER), `"HolmB"` gives Holm-Bonferroni correction, and `"Sidak"` gives Sidak correction. However, note that these options will only very rarely yield different output.

For most standard applications of sfinx, the arguments InputData and BaitVector should be sufficient. Any optimization of the other parameters is discouraged and should be explicitly reported upon communication of the results.

sfinx returns a list with two elements. The first element of the list contains a dataframe with the true-positive protein interactions that were identified by sfinx in InputData for the proteins of interest in BaitVector. The second element of the list contains a string with comments about the output and the underlying data.

sfinx(DataInputExampleFile, BaitIdentityExampleFile)

sfinx(InputData = DataInputExampleFile, BaitVector =
BaitIdentityExampleFile, ConstantLimit = FALSE, FWERType = "Sidak")