| dimReduce {netSmooth} | R Documentation |
Get lower dimension embedding
dimReduce(
x,
flavor = c("pca", "tsne", "umap"),
k = 2,
is.counts = TRUE,
ntop = 500
)
x |
gene expresison matrix [GENES x SAMPLES] |
flavor |
the algorithm to use to obtain the dimensionality reduction must be in c('pca', 'tsne', 'umap') |
k |
the number of dimensions in the reduced dimension representation |
is.counts |
logical: is 'x' counts data |
ntop |
number of most variable genes to use for dimensionality reduction |
reduced dimensionality representation