prepare_data {diceR}

Prepare data for consensus clustering

Description

Perform feature selection or dimension reduction to remove noise variables.

Usage

prepare_data(
  data,
  scale = TRUE,
  type = c("conventional", "robust", "tsne"),
  min.var = 1
)

Arguments

data

data matrix with rows as samples and columns as variables

scale

logical; should the data be centered and scaled?

type

if we use "conventional" measures (default), then the mean and standard deviation are used for centering and scaling, respectively. If "robust" measures are specified, the median and median absolute deviation (MAD) are used. Alternatively, we can apply "tsne" for dimension reduction.

min.var

minimum variability measure threshold used to filter the feature space for only highly variable features. Only features with a minimum variability measure across all samples greater than min.var will be used. If type = "conventional", the standard deviation is the measure used, and if type = "robust", the MAD is the measure used.

Details

We can apply a basic filtering method of feature selection that removes variables with low signal and (optionally) scales before consensus clustering. Or, we can use t-SNE dimension reduction to transform the data to just two variables. This lower-dimensional embedding allows algorithms such as hierarchical clustering to achieve greater performance.

Value

dataset prepared for usage in consensus_cluster

Author(s)

Derek Chiu

Examples

set.seed(2)
x <- replicate(10, rnorm(100))
x.prep <- prepare_data(x)
dim(x)
dim(x.prep)