R: Subset function for 'dnapath_list' object.

subset.dnapath_list {dnapath} | R Documentation

## Subset function for 'dnapath_list' object.

### Description

Subset function for 'dnapath_list' object.

### Usage

    ## S3 method for class 'dnapath_list'
    subset(x, pathways = NULL, genes = NULL, ...)

### Arguments

`x` | A 'dnapath_list' object from `dnapath`.
`pathways` | A set of pathways to index on. This can be (1) a vector of character strings, corresponding to pathway names or regular expressions used to find pathways, (2) a vector of indices to select pathways, (3) a vector of negative indices indicating pathways to remove, or (4) a logical (boolean) vector that is the same length of current number of pathways in `x`.
`genes` | A set of gene names to index on; exact matching is used. Only pathways containing these genes are retained.
`...` | Additional arguments are ignored.

### Value

A subset of the differential network analysis results.

### Examples

    data(meso)
    # Obtain a pathway list for this short example:
    pathway_list <- get_reactome_pathways("human", overlap_limit = NULL,
                                          min_size = 13, max_size = 19)
    # Run the differential network analysis.
    results <- dnapath(x = meso$gene_expression, pathway_list = pathway_list,
                       group_labels = meso$groups, n_perm = 5, seed = 0)
    summary(results) # Summary over all pathways in the pathway list.

    # Subset on pathways that contain "cell cycle" in its name.
    cell_cycle_pathways <- subset(results, pathways = "cell cycle")
    summary(cell_cycle_pathways)
    # Subset on pathways that contain the gene 1026 (Entrezgene ID).
    pathways_with_1026 <- subset(results, genes = "1026")
    summary(pathways_with_1026)

    # Multiple pathways and/or genes can also be specified.
    # Specifying both acts as an "OR" operation. For example, the following subset
    # will contain pathways containing the words "acetylation" or "methylation"
    # OR pathways that contain the genes "1108" or "11200".
    results_OR <- subset(results,
                         pathways = c("acetylation", "methylation"),
                         genes = c("1108", "11200"))
    summary(results_OR)
    # To subset on pathways that have both a specific pathway name AND
    # certain genes, call the subset function twice: once specifying the
    # `pathways` argument, then pass those results back into subset() with the
    # `genes` argument specified. For example:
    results_AND <- subset(results,
                          pathways = c("acetylation", "methylation"))
    results_AND <- subset(results_AND,
                          genes = c("1108", "11200"))
    summary(results_AND)

[Package dnapath version 0.7.4 Index]