pickDimReduction,matrix-method {netSmooth} | R Documentation |
Pick the dimensionality reduction method for a dataset that gives the 2D embedding with the highest entropy
## S4 method for signature 'matrix' pickDimReduction(x, flavors = c("pca", "tsne"), is.counts = TRUE) ## S4 method for signature 'SummarizedExperiment' pickDimReduction(x) ## S4 method for signature 'Matrix' pickDimReduction(x, flavors = c("pca", "tsne"), is.counts = TRUE)
x |
matrix or SummarizedExperiment object [GENES x SAMPLES] |
flavors |
list of dimensionality reduction algorithms to try. Currently the options are "pca" and "tsne" |
is.counts |
logical: is exprs count data |
name of dimensionality reduction method that gives the highest 2d entropy
x <- matrix(rnbinom(60000, size=1, prob = .1), ncol=100) pickDimReduction(x)