bootstrap_diff {ccRemover}

Calculates the difference in the loading score for cell-cycle and control genes

Description

This function is only used internally inside ccRemover. The function calcualtes the average load difference on the cell-cycle and control genes. Bootstrap resampling is then used to provide a score for each component. Please see the original manuscript for the mathematical details.

Usage

bootstrap_diff(xy, xn, nboot = 200, bar = TRUE)

Arguments

xy

The data for the genes which are annotated to the cell-cycle, i.e. those genes for which "if_cc" is TRUE.

xn

The data for the genes which are not annotated to the cell-cycle, control genes, genes for which "if_cc" is FALSE

nboot

The number of bootstrap repititions to be carried out on each iteration to determine the significance of each component.

bar

Whether to display a progress bar or not. The progress bar will not work in R-markdown enviornments so this option may be turned off. The default value is TRUE.

Value

A data frame containing the loadings for each component on the cell-cycle and control genes as well as the difference between the loadings and the bootstrapped statistic for each loading.