getGenesExpressedHigherThanExpected-methods: description of function getGenesExpressedHigherThanExpected

In stela2502/BioData: The package allows to annotate a numeric data.table with col and row data

Description

My personal VarGenes function.

Arguments

x	a SingleCells object
group	a samples grouping used to subset the original object
ref	the correlating samples group (default nUMI)
n	get the top interesting genes default= 300 (in each group!)

Details

To identify variable genes is almost the first thing that every single cell analysis strategy does. The existing VarGene function identify many highly expressed genes like ribosomal genes or mitochondrial genes if they have not been removed before.

This normally produces problems in the downstream analysis as they normally correlate with the cell cycle which most of the times is not the main interesting cellular process.

Here we try to identify genes that are correlated less to the UMI count than would be expected. The function estimates the normal correlation values for each gene count and selects for genes that are correlated to the UMI count less than other genes with the same fraction of cells expressing them.

This has proven to especially pick genes at the lower expression range like chromatin remodeling proteins or transcription factors.

No normalization is required for this function to work. It is always applied to the not normalized data.

stela2502/BioData documentation built on Feb. 23, 2022, 5:47 a.m.