R/utilities.R
CollapseSpeciesExpressionMatrix.Rd
Valuable for CITE-seq analyses, where we typically spike in rare populations of 'negative control' cells from a different species.
CollapseSpeciesExpressionMatrix( object, prefix = "HUMAN_", controls = "MOUSE_", ncontrols = 100 )
object | A UMI count matrix. Should contain rownames that start with the ensuing arguments prefix.1 or prefix.2 |
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prefix | The prefix denoting rownames for the species of interest. Default is "HUMAN_". These rownames will have this prefix removed in the returned matrix. |
controls | The prefix denoting rownames for the species of 'negative control' cells. Default is "MOUSE_". |
ncontrols | How many of the most highly expressed (average) negative control features (by default, 100 mouse genes), should be kept? All other rownames starting with prefix.2 are discarded. |
A UMI count matrix. Rownames that started with prefix
have this prefix discarded. For rownames starting with controls
, only the ncontrols
most highly expressed features are kept, and the prefix is kept. All other rows are retained.
if (FALSE) { cbmc.rna.collapsed <- CollapseSpeciesExpressionMatrix(cbmc.rna) }