analyzeFI {ASpediaFI} | R Documentation

## Functional interaction analysis of AS events

### Description

Analyze functional interactions of AS events using Discriminative Random Walk with Restart (DRaWR). It runs a DRaWR on a heterogeneous network containing genes, AS events, and pathways. It then performs GSEA on gene sets related to query genes.

### Usage

    analyzeFI(object, query, expr, ppi = NULL, pathways = NULL,
        restart = 0.7, num.folds = 5, num.feats = 100, low.expr = 1,
        low.var = NULL, prop.na = 0.05, prop.extreme = 1,
        cor.threshold = 0.3)

### Arguments

`object` | Object of class ASpediaFI
`query` | a character vector or a data frame containing query genes
`expr` | a `SummarizedExperiment` object or matrix containing gene expression profiles (FPKM)
`ppi` | an `igraph` object containing known interactions between genes. If NULL, an `igraph` object containing human gene-gene interactions will be used.
`pathways` | a GMT file or a named list of pathway gene sets. If NULL, a combined list of HALLMARK, KEGG, and REACTOME pathway gene sets will be used.
`restart` | a restart probability
`num.folds` | the number of folds for cross-validation
`num.feats` | the number of feature nodes to be retained in the final subnetwork
`low.expr` | Genes with mean expression below low.expr are excluded. AS events for corresponding genes are also excluded.
`low.var` | AS events with variance below low.var are excluded. If NULL, top 10,000 variable events are used for analysis.
`prop.na` | AS events with the higher proportion of missing values than prop.na are excluded.
`prop.extreme` | AS events with the higher proportion of extreme values (0 or 1) than prop.extreme are excluded.
`cor.threshold` | a pair of AS event and gene with Spearman's correlation greather than cor.threshold are connected in a heterogeneous network.

### Value

ASpediaFI object with results of functional interaction analysis

### References

Blatti, C. et al. (2016). Characterizing gene sets using discrminative random walks with restart on heterogeneous biological networks. Bioinformatics, 32.

### Examples

    library(limma)
    data(GSE114922.fpkm)
    data(GSE114922.psi)
    design <- cbind(WT = 1, MvsW = colData(GSE114922.psi)$condition == 'MUT')
    fit <- lmFit(log2(GSE114922.fpkm + 1), design = design)
    fit <- eBayes(fit, trend = TRUE)
    tt <- topTable(fit, number = Inf, coef = 'MvsW')
    query <- rownames(tt[tt$logFC > 1 & tt$P.Value < 0.1, ])
    head(query)
    ## Not run:
    GSE114922.ASpediaFI <- analyzeFI(
        GSE114922.ASpediaFI, query,
        GSE114922.fpkm
    )

    ## End(Not run)

[Package ASpediaFI version 1.8.0 Index]