IntersectOmicsPwyCollct {pathwayPCA} | R Documentation

## Delete -Ome symbols or IDs without matching features recorded in a given assay data frame from a pathway collection

### Description

Given a bio-assay design matrix and a `pathwayCollection` gene pathways list (each within an `Omics*`-class object), delete the genes / proteins / lipids / metabolomes / transcriptomes symbols or IDs recorded in each pathway which are not recorded in the assay data frame.

### Usage

    IntersectOmicsPwyCollct(object, trim = 3, message = TRUE, ...)

    ## S4 method for signature 'OmicsPathway'
    IntersectOmicsPwyCollct(object, trim = 3, message = TRUE, ...)

### Arguments

`object` | An object of class `OmicsPathway`, `OmicsSurv`, `OmicsReg`, or `OmicsCateg`.
`trim` | The minimum cutoff of matching -Ome measures before a pathway is excluded. Defaults to 3.
`message` | Should this function return diagnostic messages? Messages concern the percentage of genes included in the pathways list but not measured in the data, genes measured in the data but not called for in the pathways, and the number of pathways ignored due to too few number of genes present after trimming. Defaults to `TRUE`.
`...` | Dots for additional internal arguments (as necessary).

### Details

This function takes in a data frame with named columns and a `pathwayCollection` list, all through one of the `Omics*` classes. This function will then copy the pathway collection, iterate over the list of copied pathways, delete symbols or IDs from that pathway without matches from the bio-assay design matrix column names, and remove any pathways that have fewer than `trim` genes with corresponding columns in the assay. The genes not recorded in the bio-assay design matrix are removed from the copy of the pathway collection (the `trimPathwayCollection` object), but remain in the original pathway collection.

NOTE: some genes will be included in more than one pathway, so these pathways are not mutually exclusive. Further note that there may be many genes in the assay design matrix that are not included in the pathway sets, so these will not be extracted to the list. It is then vitally important to use either a very broad and generic `pathwayCollection` list or a `pathwayCollection` list that is appropriate for the assay data supplied. While you can create your own pathway lists, create proper `pathwayCollection` list objects by importing `.gmt` files with the `read_gmt` function.

### Value

A valid `Omics*`-class object. This output object will be identical to the input object, except that any genes present in the pathways list, but not present in the MS design matrix, will have been removed. Additionally, the pathway list will have the number of genes in each trimmed pathway stored as the `n_tested` object.

### Examples

    # DO NOT CALL THIS FUNCTION DIRECTLY. USE CreateOmics() INSTEAD.

    ## Not run:
      ###  Load the Example Data  ###
      data("colonSurv_df")
      data("colon_pathwayCollection")

      ###  Create an OmicsSurv Object  ###
      colon_Omics <- CreateOmics(
        assayData_df = colonSurv_df[, -(2:3)],
        pathwayCollection_ls = colon_pathwayCollection
      )

    ## End(Not run)

[Package pathwayPCA version 1.10.0 Index]