Convert SummarizedExperiment to only contain defined genes

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

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))
#> Warning: package ‘S4Vectors’ was built under R version 3.6.3
#> Warning: package ‘GenomeInfoDb’ was built under R version 3.6.3
#> Warning: package ‘DelayedArray’ was built under R version 3.6.3
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)