sfinx {sfinx} | R Documentation |
SFINX (Straightforward Filtering INdeX).
Description
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.
Usage
sfinx(InputData, BaitVector, BackgroundRatio = 5,
BackgroundIdentity = "automatic", BaitInfluence = FALSE,
ConstantLimit = TRUE, FWERType = "B")
Arguments
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 |
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. |
BackgroundIdentity |
Deprecated. A character string or character
vector describing the background projects. |
BaitInfluence |
Advanced. A logical. When TRUE, |
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 |
FWERType |
Advanced. A character string that equals |
Details
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.
Value
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.
Examples
sfinx(DataInputExampleFile, BaitIdentityExampleFile)
sfinx(InputData = DataInputExampleFile, BaitVector =
BaitIdentityExampleFile, ConstantLimit = FALSE, FWERType = "Sidak")