kmAux: This function performs 'kmeans' clustering of the subdataset...

In khazum/ccImpute: ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)

This function performs kmeans clustering of the subdataset corresponding to a given range i of PCA loadings as contained in input parameter.

Description

This function performs kmeans clustering of the subdataset corresponding to a given range i of PCA loadings as contained in input parameter.

Usage

kmAux(i, input, k, kmNStart, kmMax)

Arguments

i	number of loadings to use.
input	the matrix of all variable loadings.
k	centers (integer) parameter passed to kmeans function.
kmNStart	nstart parameter passed to kmeans function. Can be set manually. By default it is 1000 for up to 2000 cells and 50 for more than 2000 cells.
kmMax	iter.max parameter passed to kmeans function.
nCores	defines the number of cores to be used on the user's machine. If not set, 'ccImpute' will use all but one cores of your machine.
nDim	the list of containing a number of PCA loadings to use for each sub-dataset.
rand_seed	sets the seed of the random number generator. ccImpute is a stochastic method, and setting the rand_seed allows reproducibility.

Value

a list of clustering assignments for all the sub-datasets.

khazum/ccImpute documentation built on Nov. 28, 2022, 7:27 a.m.