Description Usage Arguments Value Examples
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
1 2 3 4 5 6 7 8 9 10 | limmaquickpca2go(
se,
pca_ngenes = 10000,
inputType = "ENSEMBL",
organism = "Mm",
loadings_ngenes = 500,
background_genes = NULL,
scale = FALSE,
...
)
|
se |
A |
pca_ngenes |
Number of genes to use for the PCA |
inputType |
Input format type of the gene identifiers. Deafults to |
organism |
Character abbreviation for the species, using |
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 |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.