zscoreUMI4C: Z-score calculation using residuals of trend and fit UMI4C...

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Z-score calculation using residuals of trend and fit UMI4C counts

Description

Calculates the z-score and then they are converted into one-sided P-values and adjusted for multiple testing using the method of Benjamini and Hochberg

Usage

zscoreUMI4C(
  dds,
  padj_method = "fdr",
  zscore_threshold = 2,
  padj_threshold = 0.1
)

Arguments

dds	DDS object as generated by smoothMonotoneUMI4C with the smooth monotone fit counts
padj_method	The method to use for adjusting p-values, see p.adjust. Default: fdr.
zscore_threshold	Numeric indicating the z-score threshold to use to define significant differential contacts. Default: 2.
padj_threshold	Numeric indicating the adjusted p-value threshold to use to define significant differential contacts. Default: 0.1.

Details

This function calculates the z-score for each fragment over all samples from the residuals of the symmetric monotone fit and the median absolute deviation (mad). Z-scores are then converted into one-sided P-values using the standard Normal cumulative distribution function, and these are adjusted for multiple testing using the method of Benjamini and Hochberg

Value

DDS object with zscore,pvalue and padjusted assays

Pasquali-lab/UMI4Cats documentation built on March 23, 2024, 9:42 p.m.