getbio-methods: Find Enriched Biological Terms For A Cluster
In ManuelGoepferich/LINC: co-expression of lincRNAs and protein-coding genes

Description Usage Arguments Details Value Methods Author(s) References See Also Examples

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'.

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

`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`

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.

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

signature(cluster = "LINCcluster"): (see details)

Manuel Goepferich

[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)

clusterlinc ; singlelinc ;

data(BRAIN_EXPR)

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