GSEA_ana {anamiR} | R Documentation

## This function will do function driven analysis.

### Description

This function will do GSEA analysis through the function `gage`. After obtaining the ranking of pathways, this function will choose the top five (default) pathaways, and then find the related miRNAs based on their gene set.

### Usage

    GSEA_ana(mrna_se, mirna_se, class, compare = "unpaired", eg2sym = TRUE,
      pathway_num = 5)

### Arguments

`mrna_se` | SummarizedExperiment for input format and it contains mRNA information.
`mirna_se` | SummarizedExperiment for input format, and it contains miRNA information.
`class` | string. Choose one features from all rows of phenotype data.
`compare` | character, if the length of case is the same as control, use "paired".Default is "unpaired".
`eg2sym` | logical. conversion between Entrez Gene IDs and official gene symbols for human genes.
`pathway_num` | The number of chosen pathways from the result of GSEA analysis.

### Value

list format containing both selected gene and miRNA expression data for each chosen pathway.

### See Also

`gage` for GSEA analysis.

### Examples

    require(data.table)

    ## Load example data
    aa <- system.file("extdata", "GSE19536_mrna.csv", package = "anamiR")
    mrna <- fread(aa, fill = TRUE, header = TRUE)

    bb <- system.file("extdata", "GSE19536_mirna.csv", package = "anamiR")
    mirna <- fread(bb, fill = TRUE, header = TRUE)

    cc <- system.file("extdata", "pheno_data.csv", package = "anamiR")
    pheno.data <- fread(cc, fill = TRUE, header = TRUE)

    ## adjust data format
    mirna_name <- mirna[["miRNA"]]
    mrna_name <- mrna[["Gene"]]
    mirna <- mirna[, -1]
    mrna <- mrna[, -1]
    mirna <- data.matrix(mirna)
    mrna <- data.matrix(mrna)
    row.names(mirna) <- mirna_name
    row.names(mrna) <- mrna_name
    pheno_name <- pheno.data[["Sample"]]
    pheno.data <- pheno.data[, -1]
    pheno.data <- as.matrix(pheno.data)
    row.names(pheno.data) <- pheno_name

    ## SummarizedExperiment class
    require(SummarizedExperiment)
    mirna_se <- SummarizedExperiment(
     assays = SimpleList(counts=mirna),
     colData = pheno.data)

    mrna_se <- SummarizedExperiment(
     assays = SimpleList(counts=mrna),
     colData = pheno.data)

    #table <- GSEA_ana(mrna_se = mrna_se,
    #mirna_se = mirna_se, class = "ER",
    #pathway_num = 2)

[Package anamiR version 1.12.0 Index]