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
select_features
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.
1 2 3 4 5 6 7 8 | select_genes(
cds,
fit_min = 1,
fit_max = Inf,
logmean_ul = Inf,
logmean_ll = -Inf,
top_n = NULL
)
|
cds |
the cell_data_set upon which to perform this operation. |
fit_min |
the minimum multiple of the dispersion fit calculation; default = 1 |
fit_max |
the maximum multiple of the dispersion fit calculation; default = Inf |
logmean_ul |
the maximum multiple of the dispersion fit calculation; default = Inf |
logmean_ll |
the maximum multiple of the dispersion fit calculation; default = Inf |
top |
top_n if specified, will override the fit_min and fit_max to select the top n most variant features. logmena_ul and logmean_ll can still be used. |
an updated cell_data_set object with selected features
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