SoupChannel: Construct a SoupChannel object

In constantAmateur/SoupX: Single Cell mRNA Soup eXterminator

Construct a SoupChannel object

Description

Creates a SoupChannel object that contains everything related to the soup estimation of a single channel.

Usage

SoupChannel(tod, toc, metaData = NULL, calcSoupProfile = TRUE, ...)

Arguments

tod	Table of droplets. A matrix with columns being each droplet and rows each gene.
toc	Table of counts. Just those columns of tod that contain cells.
metaData	Meta data pertaining to the cells. Optional. Must be a data-frame with rownames equal to column names of toc.
calcSoupProfile	By default, the soup profile is calculated using estimateSoup with default values. If you want to do something other than the defaults, set this to FALSE and call estimateSoup manually.
...	Any other named parameters to store.

Value

A SoupChannel object.

See Also

SoupChannelList estimateSoup setSoupProfile setClusters

Examples

#Load droplet and count tables
tod = Seurat::Read10X(system.file('extdata','toyData','raw_gene_bc_matrices','GRCh38',
                                  package='SoupX'))
toc = Seurat::Read10X(system.file('extdata','toyData','filtered_gene_bc_matrices','GRCh38',
                                  package='SoupX'))
#Default calculates soup profile
sc = SoupChannel(tod,toc)
names(sc)
#This can be suppressed
sc = SoupChannel(tod,toc,calcSoupProfile=FALSE)
names(sc)

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