CollapseSpeciesExpressionMatrix | R Documentation |
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 |
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.
## Not run:
cbmc.rna.collapsed <- CollapseSpeciesExpressionMatrix(cbmc.rna)
## End(Not run)
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