getbio-methods: Find Enriched Biological Terms For A Cluster

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

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

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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

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data(BRAIN_EXPR)

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

LINC documentation built on April 28, 2020, 6:44 p.m.