Description Usage Arguments Details Value Author(s) See Also Examples
Get or set the row subset in an instance of a SingleCellExperiment class. This is assumed to specify some interesting subset of genes to be favored in downstream analyses.
1 2 3 4 5 |
x |
A SingleCellExperiment object. |
field |
String containing the name of the field in the |
onAbsence |
String indicating an additional action to take when labels are absent:
nothing ( |
... |
Additional arguments, currently ignored. |
value |
Any character, logical or numeric vector specifying rows of |
A frequent task in single-cell data analyses is to focus on a subset of genes of interest, e.g., highly variable genes, derived marker genes for clusters, known markers for cell types. A related task is to filter out uninteresting genes such as ribosomal protein genes or mitochondrial transcripts, in which case we want to subset to exclude those genes.
These functions store a set of genes of interest inside a SingleCellExperiment
for later retrieval and use in downstream functions.
Character and numeric value
are converted to logical vectors that are parallel to the rows of x
,
allowing them to be added to the rowData
for synchronized row-level operations.
For developers, onAbsence
is provided to make it easier to mandate that x
actually has labels.
This avoids silent NULL
values that flow to the rest of the function and make debugging difficult.
For rowSubset
, a logical vector is returned specifying the rows to retain in the subset of interest.
If no subset is available, a NULL
is returned (and/or a warning or error, depending on onAbsence
).
For rowSubset<-
, a modified x
is returned a subsetting vector in its rowData
.
Aaron Lun
SingleCellExperiment, for the underlying class definition.
1 2 3 4 5 6 7 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.