ChiapetExperimentData-class {R3CPET} | R Documentation

## 3CPET used raw data

### Description

The `ChiapetExperimentData` class is a container for storing the set of raw data used by 3CPET to do the prediction.

### Usage

    ChiapetExperimentData(pet='', tfbs='', ppi=NULL,
                          ## loadPETs options
                          IsBed=TRUE, petHasHeader=FALSE, dist=1000,
                          ## loadTFBS options
                          tfbsHasHeader=FALSE,
                          ## loadPPI options
                          ppiType=c("HPRD","Biogid"),
                          filter=FALSE, term="GO:0005634", annot=NULL,
                          RPKM= NULL, threshold=1
                          )

### Arguments

`pet` | (optional) a ChIAP-PET interactions file path or a `GRanges` object. The `GRanges` object should have a column named `PET_ID`. details on the file format can be found on the `loadPETs` help page.
`tfbs` | (optional) a file path to a BED file containing transcription factors binding site or a `GRanges` object. The `GRanges` object should have a metadata column named `TF`.
`ppi` | (optional) an `igraph` object that contains a user defined protein-protein interaction network. if this parameter is not specified, the `ppiType` paramter will be used.
`IsBed` | (optional) considered only if the `pet` parameter is a file path. More info about this paramters can be found in the `loadPETs` help page.
`petHasHeader` | (optional) `logical`. Indicates if the ChIA-PET interactions file has a header or not.
`dist` | (optional) The size of the region to consider arround the center of the interacting regions.
`tfbsHasHeader` | (optional) `logical`. Indicates if the TFBS file has a header or not.
`ppiType` | (optional) considered only if the `ppi` paramter is not specified. This paramter tell the pakage to load one of the PPI (`HPRD` or `Biogrid`) shiped with the package.
`filter` | (optional) `logical`. whether of not to filter the PPI network. if the `RPKM` paramter is specified then the RPKM dataset incorporated with the package will be used. if you want to to your own way of filtering, you ca set `filter = FALSE` and pass an already processed PPI to the `ppi` paramterer.
`term` | (optional) the GO term used to filter the nodes of the PPI. this is different from the `filter` parameter. in the `filter` parameter the PPI nodes are filtered by their gene expression, while in the `term` parameter they are filtered by their genomic location. by default `"GO:0005634"` is used for filtering.
`annot` | (optional) the annotation dataset used for filtering by default the `geneLocations` is used. The user can pass a custom `data.frame`. For more details check the `loadPPI` help page.
`RPKM` | (optional) a `data.frame` object that contains the expression value of each genes. by default the `RPKMS` dataset will be used (expression value in K562 celline). For more information about the format of the data passed to this parameter please check the `loadPPI`
`threshold` | (optional) threshold value used to filter gene expression. default: 1.

### Details

The `ChiapetExperimentData` class stores the genomic coordinates of the ChIA-PET interactions, the binding sites of the different transcription factor (TFBS) and the background protein-protein interaction (PPI) network used to infer the final chromatin maintainer networks.

### Value

Constructs a `ChiapetExperimentData` object with the specified fields populated.

### Slots

pet

  : Object of class `GRanges` that stores the genomic coordinated of the interactions. it can be populated using the method `loadPETs`

tfbs

  : Object of class `GRanges` that stores the TF binding site. it can be populated using the method `loadTFBS`. NOTE: the TFBS locations can be obtained from a ChIP-Seq experiment or a motif finding software. for more information on the format of the provided data check `loadTFBS`

ppi

  Object of class `"igraph"` used as the background PPI for further analysis. it can be populated using the method `loadPPI`

.dt

  Object of class `"list"` contains a collection of `data.table` serving as indexes used internally by the package (not expected to be manipulated by the user). it can be populated using the method `createIndexes`

### Accessors

The following methods can be used to get the content of a `ChiapetExperimentData` object `x` :

  `pet(x), pet(x) <- value`: Get ChIA-PET interactions encoded as a `GRanges` object in `x`. The returned `GRanges` objects contains an attribute `PET_ID` in which the left side have an id of the form `PET#\d+\.1` and the right side interaction have an id of the form `PET#\d+\.2`. for more information check `loadPETs`

                seqnames             ranges strand |      PET_ID
                   <Rle>          <IRanges>  <Rle> | <character>
            [1]     chr1 [1240734, 1242734]      * |     PET#1.1
            [2]     chr1 [1242224, 1244224]      * |     PET#1.2
            [3]     chr1 [1282208, 1284208]      * |     PET#2.1
            [4]     chr1 [1283334, 1285334]      * |     PET#2.2
            [5]     chr1 [1370371, 1372371]      * |     PET#3.1
            [6]     chr1 [1371822, 1373822]      * |     PET#3.2

  `tfbs(x), tfbs(x) <- value`: Get the `GRanges` storing the transcription factor binding sites.

  `ppi(x), ppi(x) <- value`: Returns an `igraph` object used as a background PPI. check the `loadPPI` for more information.

### Author(s)

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

### References

Li G, Fullwood MJ, Xu H et al.ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biology 2010, 11(2):R22

Mohamed Nadhir D, Yang C et al 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process, ....

### See Also

`loadPETs`, `loadTFBS` , `loadPPI`

### Examples

    ## for example Reading ChIA-PET interaction results generated from ChIA-PET tool
    ## it should be formatted as follow:

    ## -------------------------------------------------------------------------------------------
    ## chromleft startleft endleft chromright startright endright counts      pvalue      qvalue
    ##      chr1    872113  879175       chr1     933836   938416     12 1.84529e-30 6.90983e-28
    ##      chr1    874165  879175       chr1     933340   938306     10 1.23139e-25 3.58932e-23
    ##      chr1    889676  896594       chr1     933897   938982     13 4.91311e-36 2.33753e-33
    ##      chr1    898753  907581       chr1     931133   939571     19 0.00000e+00 0.00000e+00
    ##      chr1    910103  918775       chr1     930834   938627     15 2.20004e-43 1.32812e-40
    ##      chr1    919314  922154       chr1     934212   937864      6 3.70292e-21 7.88551e-19
    ##---------------------------------------------------------------------------------------------

    ## The counts, pvalue and qvalue fields are not considered in our case
    ## it is up to the user to filter the interactions.

    ## The TFBS should be a BED file that contain the chromosome, start, end and the TF name

    ## Not run:

      ## load the different datasets
      petFile <- file.path(system.file("example",package="R3CPET"),"HepG2_interactions.txt")
      tfbsFile <- file.path(system.file("example",package="R3CPET"),"HepG2_TF.txt.gz")

      x <- ChiapetExperimentData(pet = petFile, tfbs=  tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE)
      ## build the diffrent indexes
      x <- createIndexes(x)
      x

      ## Pass objects instead of files.
      pet <- sample(pet(x),size = 20,replace = TRUE )
      tfbs <- sample(tfbs(x), size=300, replace=TRUE)
      ppi <- ppi(x)
      tst <- ChiapetExperimentData(pet = pet, tfbs= tfbs, ppi=ppi)
      tst <- createIndexes(tst)
      tst

    ## End(Not run)

[Package R3CPET version 1.12.0 Index]