bootstrap_diff

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

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

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

nboot

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 <code>TRUE</code>.

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.

Implements a method for identifying and removing
the cell-cycle effect from scRNA-Seq data. The description of the
method is in Barron M. and Li J. (2016) <doi:10.1038/srep33892>. Identifying and removing
the cell-cycle effect from single-cell RNA-Sequencing data. Submitted.
Different from previous methods, ccRemover implements a mechanism that
formally tests whether a component is cell-cycle related or not, and thus
while it often thoroughly removes the cell-cycle effect, it preserves
other features/signals of interest in the data.

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

Description

Usage

Arguments

Value