setSoupProfile: Set soup profile
In constantAmateur/SoupX: Single Cell mRNA Soup eXterminator

setSoupProfile

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 `est` containing the fraction of soup for each gene, `counts` containing the total counts for each gene and with row names corresponding to the row names of `sc$toc`.

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)

constantAmateur/SoupX documentation built on Nov. 2, 2022, 10:16 a.m.