M3D_Test_Shift: Test for horizontal shift.

In tallulandrews/M3Drop: Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Test for horizontal shift.

Description

Tests whether a given set of genes are significantly shifted to the left or right of the Michaelis-Menten curve.

Usage

  M3DropTestShift(expr_mat, genes_to_test, name="", background=rownames(expr_mat), suppress.plot=FALSE)

Arguments

expr_mat	a numeric matrix of normalized (not log-transformed) expression values, columns = samples, rows = genes.
genes_to_test	vector of gene names to test.
name	string used to title the plot.
background	vector of gene names to test against. (default = all genes)
suppress.plot	logical, whether to the fitted Michaelis-Menten curve and highlight the given set of genes to test.

Details

Fits a Michaelis-Menten function to the dropout-rate of the provided data, then tests whether a given set of genes (eg. pseudogenes) is significantly shifted left or right of the curve. Horizontal residuals are calculated as :

\log_{10} S - \log_{10} \frac{K*(1-P)}{P}

. Uses a Wilcox rank-sum test/Mann-Whitney U test to compare the residuals for the given genes to the residuals for all genes.

Value

A one row dataframe with columns: sample (median horizontal residual of genes in the test set), pop (median horizontal residual of genes in the background set), p.value

Examples

  library(M3DExampleData)
  gene_set <- c("Dppa2","Tdgf1","Rnf130","Tet1","Uhrf1","Pttg1","Zfp600","Stat1")
  shift_output <- M3DropTestShift(Mmus_example_list$data, gene_set)

tallulandrews/M3Drop documentation built on March 6, 2024, 1:49 a.m.