loadPPI-methods {R3CPET} | R Documentation

## Setting the background protein-protein interaction

### Description

This method enables the user to define the PPI network as a background network. The user can provide his own PPI or use the `HPRD` or the `Biogrid` PPI incorporated in the package.

### Usage

    ## S4 method for signature 'ChiapetExperimentData'
    loadPPI(object,type=c("HPRD","Biogid"),customPPI= NULL,
                  filter=FALSE, term ="GO:0005634", annot=NULL,
                  RPKM= NULL, threshold=1 )

### Arguments

`object` | a `ChiapetExperimentData` to load the PPI into as an `igraph` object
`type` | if `customPPI = NULL`, this parameter indicats which of the available PPI to use `HPRD` or `Biogrid` (build 3.2.100). by default, the `HPRD` network is used.
`customPPI` | If the user wants to use his own PPI interaction network (for example for another species), he can provide an `igraph` object or a path to an `"ncol"` formatted graph (a file with two columns indicating the interacting parts and an optional third column to indicate the weight). It is preferred that the user provides an `igraph` object, to avoid any problems when parsing the `"ncol"` file.
`filter` | This parameter indicates whether the user want to filter the selected PPI or not. `filter = FALSE` means that the PPI (provided by the user or by the `HPRD` and `Biogrid` networks) will be used as is. if `filter = TRUE`,the proteins in the PPI will be filtered according to their position in cell ( by default proteins located in the nucleus are kept and the other removed). In addition to the filtering by location, if the user wants just to keep the proteins that show a certain amount of expression he can provide a gene expression table to the `RPKM` parameter and set the `threshold` for filtering.
`term` | The GO term used to for filtering. By default, only protein that are located in the nucleus are kept (`term = "GO:0005634"`). If the user want to use another annotation table he can pass a `data.frame` object to the parameter `annot`.
`annot` | If the user wants to provide his own annotation data-set, he can pass a `data.frame` object to this parameter. The passed `data.frame` should have at least two columns named respectively: `geneSymbol` that contains the gene names, and `cellular_component_term` that contain the term.
        geneSymbol                    cellular_component_term
        FAU Ribosome      (GO:0005840); Nucleolus (GO:0005730)
        ALDH3A1   Cytoplasm (GO:0005737); Nucleus (GO:0005634)
        ASCL1     Nucleus (GO:0005634); Cytoplasm (GO:0005737)
`RPKM` | A `data.frame` that contains the expression of each gene in the PPI. The `data.frame` should at least have 2 columns. The first one contains the gene symbol (should be the same as the one used in the PPI) and the second gives the expression.
`threshold` | Threshold value used to filter gene expression. All genes with expression value less than `threshold` are removed.

### Value

A `ChiapetExperimentData` object in which the `ppi` slot is populated as an `igraph` object filtered according to the specified conditions.

### Author(s)

Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)

### References

Prasad, T. S. K. et al. (2009) Human Protein Reference Database - 2009 Update. Nucleic Acids Research. 37, D767-72.

Chatr-Aryamontri A, Breitkreutz BJ et al. The BioGRID Interaction Database: 2013 update. Nucleic Acids Res. 2012 Nov 30

M.N Djekidel et al,3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process, in press, 2015

### See Also

`ChiapetExperimentData`, `loadTFBS` , `loadPETs`, `createIndexes`

### Examples

    ## Create a ChiapetExperimentData object
    x <- ChiapetExperimentData(ppiType= "HPRD")

    ## Loading the default HPRD network without filtering

    x <- loadPPI(x,type="HPRD")
    ppi(x)

    ## Using the HPRD network and filtering using the GO:0005634
    x <- loadPPI(x,type="HPRD", filter=TRUE)
    ppi(x)

    data(RPKMS)
    x <- loadPPI(x,type="HPRD",filter=TRUE,annot= NULL, RPKM= RPKMS, threshold = 5)
    ppi(x)

[Package R3CPET version 1.18.0 Index]