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,
       translate      = "mygene",
       annotateFrom   = 'enrichGO',
       verbose        = TRUE,
       ...)

Arguments

cluster

a 'LINCcluster'. The number of co-expressed genes has to be sufficient.

translate

one of c("mygene", "none"). For "mygene" the correspondent package will be loaded for gene id translation from Ensembl to Entrez. For "none" no translation will be called.

annotateFrom

a function which will derive significant biological terms based on the set of co-expressed genes from a gene annotation resource.

verbose

whether to give messages about the progression of the function TRUE or not FALSE

...

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", "enrichKEGG", "enrichPathway", "enrichDO") [1]. The gene system of the input object has to be either Entrez or Ensembl. For Ensembl mygene [2] will be loaded in order to translate gene ids. Importanly, functions from clusterProfiler [1] require Entrez 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)

[2] Mark A, Thompson R and Wu C (2014). mygene: Access MyGene.Info_ services. R package version 1.8.0. (https://www.bioconductor.org/packages/release/bioc/html/mygene.html)

See Also

clusterlinc ; singlelinc ; overlaylinc

Examples

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data(BRAIN_EXPR)

## Find the enriched cellular components for each query in the cluster 
crbl_cc <- getbio(crbl_cluster, translate = 'none', ont = "CC")
plotlinc(crbl_cc)

ManuelGoepferich/LINC_before_DEVEL documentation built on May 9, 2017, 8:32 a.m.