Description Usage Arguments Value
Monocle3 aims to learn how cells transition through a
biological program of gene expression changes in an experiment. Each cell
can be viewed as a point in a high-dimensional space, where each dimension
describes the expression of a different gene. Identifying the program of
gene expression changes is equivalent to learning a trajectory that
the cells follow through this space. However, the more dimensions there are
in the analysis, the harder the trajectory is to learn. Fortunately, many
genes typically co-vary with one another, and so the dimensionality of the
data can be reduced with a wide variety of different algorithms. Monocle3
provides two different algorithms for dimensionality reduction via
reduce_dimensions
(UMAP and tSNE). The function
calculate_dispersion
is an optional step in the trajectory building
process before preprocess_cds
. After calculating dispersion for
a cell_data_set using the calculate_gene_dispersion
function, the
select_genes
function allows the user to identify a set of genes
that will be used in downstream dimensionality reduction methods. These
genes and their disperion and mean expression can be plotted using the
plot_gene_dispersion
function.
1 2 3 4 5 6 7 8 | calculate_gene_dispersion(
cds,
q = 3,
id_tag = "id",
symbol_tag = "gene_short_name",
method = "m3addon",
removeOutliers = T
)
|
cds |
the cell_data_set upon which to perform this operation. |
q |
the polynomial degree; default = 3. |
id_tag |
the name of the feature data column corresponding to the unique id - typically ENSEMBL id; default = "id". |
symbol_tag |
the name of the feature data column corresponding to the gene symbol; default = "gene_short_name". |
an updated cell_data_set object with dispersion and mean expression saved
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