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Calculate DGEs between cells based on Mann Whitney stats

rs_calculate_dge_mann_whitney.Rd

The function will take two sets of cell indices and calculate the differential gene expression based on the Mann Whitney test between the two groups.

Usage

rs_calculate_dge_mann_whitney(
  f_path,
  cell_indices_1,
  cell_indices_2,
  min_prop,
  alternative,
  verbose
)

Arguments

f_path

String. Path to the counts_cells.bin file.

cell_indices_1

Integer. Index positions (0-indexed) of the cells of group 1.

cell_indices_2

Integer. Index positions (0-indexed) of the cells of group 2.

min_prop

Minimum proportion of expression in at least one of the two groups to be tested.

alternative

String. One of c("twosided", "greater", "less"). Null hypothesis.

verbose

Boolean. Controls verbosity of the function.

Value

A list with the following elements

  • lfc - Log fold changes between the two groups.

  • prop1 - Proportion of cells expressing the gene in group 1.

  • prop2 - Proportion of cells expressing the gene in group 2.

  • z_scores - Z-scores based on the Mann Whitney statistic.

  • p_values - P-values of the Mann Whitney statistic.

  • fdr - False discovery rate after BH adjustment

  • genes_to_keep - Boolean indicating which genes were tested.