results_expr {RegEnrich} | R Documentation

## Result accessor functions

### Description

- results_expr accesses raw expression data.

- results_DEA accesses results from differential expression analysis.

- results_topNet accesses results from network inference.

- retults_enrich accesses results from FET/GSEA enrichment analysis.

- results_score accesses results from regulator scoring and ranking.

### Usage

    results_expr(object)

    results_DEA(object)

    results_topNet(object)

    results_enrich(object)

    results_score(object)

### Arguments

`object` | RegenrichSet object.

### Value

results_expr retures an expression matrix.

results_DEA returns a list result of differentila analysis.

results_topNet returns a TopNetwork object.

results_enrich returns an Enrich object by either FET or GSEA method.

results_score returns an data frame of summarized ranking scores of regulators.

### Examples

    # library(RegEnrich)
    data("Lyme_GSE63085")
    data("TFs")

    data = log2(Lyme_GSE63085$FPKM + 1)
    colData = Lyme_GSE63085$sampleInfo

    # Take first 2000 rows for example
    data1 = data[seq(2000), ]

    design = model.matrix(~0 + patientID + week, data = colData)

    # Initializing a 'RegenrichSet' object
    object = RegenrichSet(expr = data1,
                          colData = colData,
                          method = 'limma', minMeanExpr = 0,
                          design = design,
                          contrast = c(rep(0, ncol(design) - 1), 1),
                          networkConstruction = 'COEN',
                          enrichTest = 'FET')

    # Differential expression analysis
    object = regenrich_diffExpr(object)
    results_expr(object)
    results_DEA(object)

    # Network inference using 'COEN' method
    object = regenrich_network(object)
    results_topNet(object)

    # Enrichment analysis by Fisher's exact test (FET)
    object = regenrich_enrich(object)
    results_enrich(object)

    # Regulators ranking
    object = regenrich_rankScore(object)
    results_score(object)

[Package RegEnrich version 1.2.0 Index]