expandClusters

Given a clustering of cells and soup counts calculated for each of those clusters, determines a most likely allocation of soup counts at the cell level.

Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) <doi:10.1101/303727>.

Matthew Young

SoupX

Single Cell mRNA Soup eXterminator

expandClusters function

<dl><dt>clustSoupCnts</dt>
<dd>Matrix of genes (rows) by clusters (columns) where counts are number of soup counts for that gene/cluster combination.</dd>
<dt>cellObsCnts</dt>
<dd>Matrix of genes (rows) by cells (columns) giving the observed counts</dd>
<dt>clusters</dt>
<dd>Mapping from cells to clusters.</dd>
<dt>cellWeights</dt>
<dd>Weighting to give to each cell when distributing counts. This would usually be set to the number of expected soup counts for each cell.</dd>
<dt>verbose</dt>
<dd>Integer giving level of verbosity. 0 = silence, 1 = Basic information, 2 = Very chatty, 3 = Debug.</dd></dl>

Arguments

Expands soup counts calculated at the cluster level to the cell level — expandClusters

<dl>

<dt>clustSoupCnts</dt>
<dd>Matrix of genes (rows) by clusters (columns) where counts are number of soup counts for that gene/cluster combination.</dd>


<dt>cellObsCnts</dt>
<dd>Matrix of genes (rows) by cells (columns) giving the observed counts</dd>


<dt>clusters</dt>
<dd>Mapping from cells to clusters.</dd>


<dt>cellWeights</dt>
<dd>Weighting to give to each cell when distributing counts. This would usually be set to the number of expected soup counts for each cell.</dd>


<dt>verbose</dt>
<dd>Integer giving level of verbosity. 0 = silence, 1 = Basic information, 2 = Very chatty, 3 = Debug.</dd>

</dl>

expandClusters: Expands soup counts calculated at the cluster level to the cell level

Description

Usage

Value

Arguments