M3D_Test_Shift: Test for horizontal shift.
In tallulandrews/M3D: Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Description Usage Arguments Details Value Examples

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

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

`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.

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( (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.

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

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