setSoupProfile {SoupX} | R Documentation |
Set soup profile
Description
Manually sets or updates the soup profile for a SoupChannel object.
Usage
setSoupProfile(sc, soupProfile)
Arguments
sc |
A SoupChannel object. |
soupProfile |
A data.frame with columns |
Value
An updated SoupChannel object with the soup profile set.
Examples
#Suppose only table of counts is available
toc = Seurat::Read10X(system.file('extdata','toyData','filtered_gene_bc_matrices','GRCh38',
package='SoupX'))
#Suppress calculating soup profile automatically
sc = SoupChannel(toc,toc,calcSoupProfile=FALSE)
#And add manually
rowSums = Matrix::rowSums
soupProf = data.frame(row.names = rownames(toc),est=rowSums(toc)/sum(toc),counts=rowSums(toc))
sc = setSoupProfile(sc,soupProf)
[Package SoupX version 1.6.2 Index]