singlelinc-methods: Co-Expression Analysis Of A Single ncRNA Gene

In ManuelGoepferich/LINC_before_DEVEL: annotation of noncoding RNAs and coexpressed genes

Description

The function singlelinc perfroms co-expression analysis for a single query. An input LINCmatrix will be converted to a LINCsingle object. As a first step (I) a set of co-expressed protein-coding genes of a query is determined. Secondly, (II) biological terms related to the these genes are derived. The result will show the co-expression for the query.

Usage

singlelinc(input,
           query,
        onlycor = FALSE,
        testFun = cor.test,
    alternative = "greater",
      threshold = 0.05,
        underth = TRUE,
      coExprCut,
  handleGeneIds = TRUE,
  annotateFrom  = 'enrichGO',
        verbose = TRUE,
        ...)

Arguments

input	an object of the class LINCmatrix
query	the name of the (ncRNA) gene to be evaluated; has to be present in input
onlycor	if TRUE co-expression will be decided based on absolute correlation values from the input LINCmatrix object. If FALSE co-expressed genes will be selected based on p-values from the correlation test.
testFun	a function to test the robustness of correlations. User-defined functions are allowed. The expected output is a p-value.
alternative	one of c("two.sided", "less", "greater"). This argument indicates the alternative in the correlation test. "less" instead of "greater" can be used for negative correlations.
threshold	a single number representing the threshold for selecting co-expressed genes
underth	if TRUE values lower than the threshold will be considered (intended for p-values). If FALSE values higher tahn the threshold will be considered (intended for absolute correlations)
coExprCut	a single integer indicating the maximal number of co-expressed genes to select. In case too many genes fulfill the supplied threshold criterion their number can be reduced by this argument.
handleGeneIds	if TRUE attempt to recognize and handle issues with incompatible gene systems. If FALSE skip this section.
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 cor.test and functions from clusterProfiler

Details

In comparison to the function clusterlinc this function will provide more flexibility in terms of the selection of co-expressed genes. The option onlycor = TRUE in combination with a suitable threshold can be used to choose co-expressed protein-coding genes based on the correlation values inherited from the input LINCmatrix object. For this to work it is required to set underth = FALSE because then, values higher than the threshold will be picked. By default, co-expression depnds on the p-values from the correlation test (stats::cor.test) which demonstrate the robustness of a given correlation between two genes. A user-defined test function supplied in testFun requires the formal arguments x, y, method and use. Moreover, the p-values of the output should be accessible by $pvalue. The number of co-expressed genes can be restricted not only by threshold, but also by coExprCut. The value n for coExprCut = n will be ignored in case the number of genes which fulfill the threshold criterion is smaller than n. handleGeneIds = FALSE should only be used for an input with Entrez gene ids. Options for annotateFrom are for example: ReactomePA::enrichPathway(), clusterProfiler::enrichGO or clusterProfiler::enrichKEGG. Further arguments (...) are inteded to be passed to the called annotateFrom function. annotateFrom = 'enrichGO', ont = "CC" will call the subontology "Cellular Component" from GO. For more details see the documentation ofclusterProfiler.

Value

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

results	a list of four entries: $query, the queried gene, $bio, a list of biological terms and their p-values, $cor, absolute correlations of co-expressed genes, $pval, p-values from the correlation test of co-expressed genes
assignment	a character vector of protein-coding genes
correlation	a list of $single, the correlation of the query to protein-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(input = "LINCmatrix")

(see details)

Compatibility

plotlinc(LINCsingle, ...)), ...

Author(s)

Manuel Goepferich

See Also

linc ; singlelinc

Examples

data(BRAIN_EXPR)

# selection based on absolute correlation
meg3 <- singlelinc(crbl_matrix, query = "55384", onlycor = TRUE, underth = FALSE, threshold = 0.5)
plotlinc(meg3)

# get biological processes from 'Gene Ontology'
meg3 <- singlelinc(crbl_matrix, query = "55384", threshold = 0.00005, ont = 'BP')
plotlinc(meg3)

# get enriched pathways from 'ReatomePA'
meg3 <- singlelinc(crbl_matrix, query = "55384", onlycor = TRUE, underth = FALSE, threshold = 0.5,
                   annotateFrom = 'enrichPathway')
plotlinc(meg3)

ManuelGoepferich/LINC_before_DEVEL documentation built on May 7, 2019, 2:46 p.m.