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

View source: R/xCell.R

xCellSignifcanceRandomMatrixR Documentation

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.


dviraran/xCell documentation built on May 3, 2024, 7:17 p.m.