xCellSignifcanceRandomMatrix: Calculate significance p-values for the null hypothesis that...

In IOBR/IOBR: Immune Oncology Biological Research

Calculate significance p-values for the null hypothesis that the cell type is not present in the mixture using a random matrix.

Description

xCellSignifcanceRandomMatrix Returns the FDR adjusted p-values of the chance that the cell is not present in the mixture.

Usage

xCellSignifcanceRandomMatrix(
  scores,
  expr,
  spill,
  alpha = 0.5,
  nperm = 250,
  file.name = NULL
)

Arguments

scores	the xCell scores.
expr	the input expression matrix.
spill	the Spillover object for adjusting the scores.
alpha	a value to override the spillover alpha parameter. Deafult = 0.5
nperm	number of samples in the shuffled matrix, default = 250
file.name	file name to write the p-values table.

Value

a list with the p-values, the xcell scores of the shuffled data and the shuffled expression matrix.

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.