extractGeneExpression {IsoformSwitchAnalyzeR} | R Documentation |
Extract replicate gene raw unnormalised counts or expression from a switchAnalyzeRlist object using all the annotation fixes employed in creating the switchAnalyzeRlist.
extractGeneExpression( switchAnalyzeRlist, extractCounts = TRUE, addGeneNames = TRUE, addIdsAsColumns = TRUE )
switchAnalyzeRlist |
A |
extractCounts |
A logic to indicate whether to extract raw unnormalised counts (if TRUE, default) or expression estimates (if FALSE). |
addGeneNames |
A logic to indicate whether to add gene_names to the expression matrix (if TRUE, default) or not (if FALSE). |
addIdsAsColumns |
A logic to indicate whether to add the gene identifiers to the data.frame as collumns (if TRUE, default) or rownames (if FALSE). |
The count matrix obtained if extractCounts=TRUE
is the same as would be obtained by running tximport with countsFromAbundance="scaledTPM" which are suitable both for analysis of differential expression and usage.
A data.frame with the replicate count/abundance estimates as well as gene_id (and gene_name if extractCounts=TRUE
)
Kristoffer Vitting-Seerup
Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).
data("exampleSwitchList") ### Raw count matrix geneCountMatrix <- extractGeneExpression( exampleSwitchList, extractCounts = TRUE ) ### Raw count matrix - with ids as rownames instead of columns geneCountMatrix <- extractGeneExpression( exampleSwitchList, extractCounts = TRUE, addIdsAsColumns = FALSE ) ### Abundance matrix geneExpresionMatrix <- extractGeneExpression( exampleSwitchList, extractCounts = FALSE )