getbio-methods {LINC} | R Documentation

## Find Enriched Biological Terms For A Cluster

### Description

The function provides an interface to the `clusterProfiler` package. For each query in a cluster it seeks the biological terms that can be associated with the co-expressed genes, respectively. The input for `getbio` is of the class `'LINCcluster'`.

### Usage

    getbio(cluster,
           enrichFun   = 'enrichGO',
           ont = "BP",
           ...)

### Arguments

`cluster` | a `'LINCcluster'`. The number of co-expressed genes has to be sufficient.
`enrichFun` | a function given as character string which will derive significant biological terms based on the set of co-expressed genes from a gene annotation resource. Supported functions are: `c("enrichGO", "enrichPathway", "enrichDO")`
`ont` | a subontology, only used for `enrichFun = 'enrichGO'`. This has to be one of `"MF", "BP", "CC"`.
`...` | further arguments, mainly for functions from `clusterProfiler`

### Details

In contrast to the function `singlelinc` here, a group of queries, those present in the input cluster, will be analyzed for enriched biological terms. The annotation function can be one of `c("enrichGO", "enrichPathway", "enrichDO")`. [1] The gene system of the input object has to be translated for the enrichment function in case genes are not given as Entrez ids. The function `clusterProfiler:bitr` [2] will be used in order to translate gene ids.

### Value

an object of the class 'LINCmatrix' (S4) with 6 `Slots`

`results` | a `list` containing the identified enriched biological terms plus their respective p-values
`assignment` | a `character` vector of protein-coding genes
`correlation` | a `list` of `cormatrix`, the correlation of non-coding to protein-coding genes and `lnctolnc`, the correlation of non-coding to non-coding genes
`expression` | the original expression matrix
`history` | a storage environment of important methods, objects and parameters used to create the object
`linCenvir` | a storage environment ensuring the compatibility to other objects of the `LINC` class

### Methods

`signature(cluster = "LINCcluster")`

  (see details)

### Author(s)

Manuel Goepferich

### References

[1] Yu G, Wang L, Han Y and He Q (2012). "clusterProfiler: an R package for comparing biological themes among gene clusters." OMICS: A Journal of Integrative Biology, 16(5), pp. 284-287. (https://www.bioconductor.org/packages/release/bioc/html/clusterProfiler.html)

### See Also

`clusterlinc` ; `singlelinc` ;

### Examples

    data(BRAIN_EXPR)

    ## Find the enriched cellular components for each query in the cluster
    crbl_cc <- getbio(crbl_cluster, ont = "CC")
     plotlinc(crbl_cc)

[Package LINC version 1.12.0 Index]