Functional interpretation of the principal components, based on simple overrepresentation analysis

Extracts the genes with the highest loadings for each principal component, and performs functional enrichment analysis on them using the simple and quick routine provided by the limma package

limmaquickpca2go(
  se,
  pca_ngenes = 10000,
  inputType = "ENSEMBL",
  organism = "Mm",
  loadings_ngenes = 500,
  background_genes = NULL,
  scale = FALSE,
  ...
)

Arguments

se

A DESeq2::DESeqTransform() object, with data in assay(se), produced for example by either DESeq2::rlog() or DESeq2::varianceStabilizingTransformation()

pca_ngenes

Number of genes to use for the PCA

inputType

Input format type of the gene identifiers. Deafults to ENSEMBL, that then will be converted to ENTREZ ids. Can assume values such as ENTREZID,GENENAME or SYMBOL, like it is normally used with the select function of AnnotationDbi

organism

Character abbreviation for the species, using org.XX.eg.db for annotation

loadings_ngenes

Number of genes to extract the loadings (in each direction)

background_genes

Which genes to consider as background.

scale

Logical, defaults to FALSE, scale values for the PCA

...

Further parameters to be passed to the goana routine

Value

A nested list object containing for each principal component the terms enriched in each direction. This object is to be thought in combination with the displaying feature of the main pcaExplorer() function

Examples

library("airway")
library("DESeq2")
library("limma")
#> 
#> Attaching package: ‘limma’
#> The following object is masked from ‘package:DESeq2’:
#> 
#>     plotMA
#> The following object is masked from ‘package:BiocGenerics’:
#> 
#>     plotMA
data("airway", package = "airway")
airway
#> class: RangedSummarizedExperiment 
#> dim: 63677 8 
#> metadata(1): ''
#> assays(1): counts
#> rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
#>   ENSG00000273493
#> rowData names(10): gene_id gene_name ... seq_coord_system symbol
#> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
#> colData names(9): SampleName cell ... Sample BioSample
dds_airway <- DESeqDataSet(airway, design = ~ cell + dex)
if (FALSE) { # \dontrun{
rld_airway <- rlogTransformation(dds_airway)
goquick_airway <- limmaquickpca2go(rld_airway,
                                   pca_ngenes = 10000,
                                   inputType = "ENSEMBL",
                                   organism = "Hs")
} # }