convertSESubsetGenes {bigPint} | R Documentation

## Convert SummarizedExperiment to only contain defined genes

### Description

Reduce a SummarizedExperiment object so that it only now contains a subset of genes.

### Usage

    convertSESubsetGenes(dataSE, geneList)

### Arguments

`dataSE` | SUMMARIZEDEXPERIMENT | Summarized experiment format that can be used in lieu of data and dataMetrics
`geneList` | CHARACTER ARRAY | List of gene IDs to remain in dataSE

### Value

A new dataSE object that is a subset of the input dataSE in that it now only contains the user-specified list of genes.

### Examples

    # Example: Read in example SummarizedExperiment object that originally
    # contains 5604 genes. Reduce it to now only contain ten genes (specifically
    # the ones with the lowest FDR).

    suppressMessages(library(dplyr))
    suppressMessages(library(SummarizedExperiment))
    data(se_soybean_ir_sub)
    geneList <- as.data.frame(rowData(se_soybean_ir_sub)) %>%
        arrange(N_P.FDR) %>% filter(row_number() <= 10)
    geneList <- geneList[,1]
    se_soybean_ir_sub_2 <- convertSESubsetGenes(se_soybean_ir_sub, geneList)

[Package bigPint version 1.4.0 Index]