suggest_cutoff: Suggest cutoff of library size

In ybai3/SCQC: Single Cell Sequencing Data Quality Control

Description

This function suggests cutoff of library size for library-wise screening by an empirical criteria. The cutoff is found by seeking first three bins with wilcoxon P-value lower than multiple test corrected P-value at 0.05. Although the library-wise cutoff can be suggested by this function, we still recommend users to look at the boxplot made by corcoefplot() function for double check.

Usage

suggest_cutoff(rcleaned_matrix,wilcox_p)

Arguments

rcleaned_matrix	Gene-wise cleaned countmatrix, containing both of housekeeping and non-housekeeping data
wilcox_p	Wilcoxon P-value in gene-wise screening. Can be found in the output list of genewise function.

Value

Suggested library size with its quantile across libraries.

Examples

suggest_cutoff(rcleaned_matrix,wilcox_p)



{ ~library-wise cutoff }

ybai3/SCQC documentation built on May 19, 2019, 9:40 p.m.