Clustering miRNAs-genes pairs
isoNetwork(mirna_rse, gene_rse, summarize = NULL, target = NULL, org = NULL, enrich = NULL, genename = "ENSEMBL", min_cor = -0.6, min_fc = 0.5)
mirna_rse | SummarizedExperiment::SummarizedExperiment with miRNA information. See details. |
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gene_rse | SummarizedExperiment::SummarizedExperiment with gene information. See details. |
summarize | Character column name in |
target | Matrix with miRNAs (columns) and genes (rows) target prediction (1 if it is a target, 0 if not). |
org | AnnotationDbi::AnnotationDb obejct. For example:(org.Mm.eg.db) |
enrich | The output of |
genename | Character keytype of the gene names in gene_rse object. |
min_cor | Numeric cutoff to consider a miRNA to regulate a target. |
min_fc | Numeric cutoff to consider as the minimum log2FoldChange between groups to be considered in the analysis. |
list with network information
This function will correlate miRNA and gene expression data using
a specific metadata variable to group samples and detect pattern
of expression that will be annotated with GO terms.
mirna_rse and gene_rse can be created using the following code:
mi_rse = SummarizedExperiment(assays=SimpleList(norm=mirna_matrix), colData, metadata=list(sign=mirna_keep))
where, mirna_matrix
is the normalized counts expression,
colData
is the metadata information and mirna_keep
the list of miRNAs to be used by this function.
# library(org.Mm.eg.db) # library(clusterProfiler) data(isoExample) # ego <- enrichGO(row.names(assay(gene_ex_rse, "norm")), # org.Mm.eg.db, "ENSEMBL", ont = "BP") data <- isoNetwork(mirna_ex_rse, gene_ex_rse, ma_ex, org = ego)#> Error: summarize %in% names(colData(mirna_rse)) are not all TRUEisoPlotNet(data)#> Error in obj$analysis: object of type 'closure' is not subsettable