kmeans_haystack

kmeans_haystack.matrix

kmeans_haystack.data.frame

a matrix or other object from which coordinates of cells can be extracted.

further parameters passed down to methods.

column index or name of matrix for x-axis coordinates.

dim1

column index or name of matrix for y-axis coordinates.

dim2

Function for k-means clustering of genes according to their expression distribution in 2D or multi-dimensional space

Identification of differentially expressed genes (DEGs) is a key step in single-cell
transcriptomics data analysis. 'singleCellHaystack' predicts DEGs without relying on
clustering of cells into arbitrary clusters. Single-cell RNA-seq (scRNA-seq) data is
often processed to fewer dimensions using Principal Component Analysis (PCA) and
represented in 2-dimensional plots (e.g. t-SNE or UMAP plots). 'singleCellHaystack'
uses Kullback-Leibler divergence to find genes that are expressed in subsets of cells
that are non-randomly positioned in a these multi-dimensional spaces or 2D representations.
For the theoretical background of 'singleCellHaystack' we refer to
Vandenbon and Diez (Nature Communications, 2020) <doi:10.1038/s41467-020-17900-3>.

Alexis Vandenbon

singleCellHaystack

Finding Needles (=differentially Expressed Genes) in Haystacks
(=single Cell Data)

Diego Diez

kmeans_haystack function

<dl><dt>x</dt>
<dd>a matrix or other object from which coordinates of cells can be extracted.</dd>
<dt>...</dt>
<dd>further parameters passed down to methods.</dd>
<dt>dim1</dt>
<dd>column index or name of matrix for x-axis coordinates.</dd>
<dt>dim2</dt>
<dd>column index or name of matrix for y-axis coordinates.</dd></dl>

Arguments

Function for k-means clustering of genes according to their expression distribution in 2D or multi-dimensional space — kmeans_haystack

<dl>

<dt>x</dt>
<dd>a matrix or other object from which coordinates of cells can be extracted.</dd>


<dt>...</dt>
<dd>further parameters passed down to methods.</dd>


<dt>dim1</dt>
<dd>column index or name of matrix for x-axis coordinates.</dd>


<dt>dim2</dt>
<dd>column index or name of matrix for y-axis coordinates.</dd>

</dl>

kmeans_haystack: Function for k-means clustering of genes according to their expression distribution in 2D or multi-dimensional space

Description

Usage

Arguments