limmaquickpca2go {pcaExplorer} | R Documentation

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

### Description

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

### Usage

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

### Arguments

`se` | A `DESeqTransform` object, with data in `assay(se)`, produced for example by either `rlog` or `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 topGO 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)
    data(airway)
    airway
    dds_airway <- DESeqDataSet(airway, design= ~ cell + dex)
    ## Not run:
    rld_airway <- rlogTransformation(dds_airway)
    goquick_airway <- limmaquickpca2go(rld_airway,
                                       pca_ngenes = 10000,
                                       inputType = "ENSEMBL",
                                       organism = "Hs")

    ## End(Not run)

[Package pcaExplorer version 2.14.2 Index]