EventCoverage: Generate event coverage analysis and visualization for...

In ZetaSuite: Analyze High-Dimensional High-Throughput Dataset and Quality Control Single-Cell RNA-Seq

Generate event coverage analysis and visualization for alternative splicing data.

Description

This function analyzes event coverage across Z-score thresholds and generates visualizations to compare positive and negative control samples. It calculates the proportion of readouts that exceed different Z-score thresholds for each gene, creating the foundation for zeta score calculations.

Usage

EventCoverage(ZscoreVal, negGene, posGene, binNum, combine = TRUE)

Arguments

ZscoreVal	A matrix of Z-scores where rows represent genes and columns represent readouts/conditions. This is typically the output from the Zscore() function.
negGene	A data frame or matrix containing negative control gene/siRNA identifiers. The first column should contain gene/siRNA names that match the row names in ZscoreVal.
posGene	A data frame or matrix containing positive control gene/siRNA identifiers. The first column should contain gene/siRNA names that match the row names in ZscoreVal.
binNum	The number of bins to divide the Z-score range. Recommended value is 100. The function creates Z-score thresholds from the 0.00001 to 0.99999 quantiles of the data.
combine	Logical. Whether to combine the negative and positive Z-score ranges. Default is TRUE. When TRUE, uses symmetric ranges around zero; when FALSE, uses separate ranges for negative and positive values.

Details

The function performs the following steps:

1. Determines Z-score thresholds based on data quantiles and binNum

2. For each gene and threshold, calculates the proportion of readouts that exceed (increase) or fall below (decrease) the threshold

3. Separates data into negative and positive control groups

4. Generates jitter plots comparing event coverage between control groups

5. Returns both data matrices and visualization plots

The event coverage matrices can be used as input for SVM analysis and zeta score calculations.

Value

A list containing two sublists:

ECdataList

A list with the following components: ZseqList: A data frame with Z-score thresholds for decrease (Zseq_D) and increase (Zseq_I) directions EC_N_I: Event coverage matrix for negative controls in increase direction EC_N_D: Event coverage matrix for negative controls in decrease direction EC_P_I: Event coverage matrix for positive controls in increase direction EC_P_D: Event coverage matrix for positive controls in decrease direction

ECplotList

A list with two ggplot objects: EC_jitter_D: Jitter plot showing event coverage for decrease direction EC_jitter_I: Jitter plot showing event coverage for increase direction

Author(s)

Yajing Hao, Shuyang Zhang, Junhui Li, Guofeng Zhao, Xiang-Dong Fu

Examples

data(countMat)
data(negGene)
data(posGene)
ZscoreVal <- Zscore(countMat, negGene)
ECList <- EventCoverage(ZscoreVal, negGene, posGene, binNum=100, combine=TRUE)

ZetaSuite documentation built on Nov. 5, 2025, 6:37 p.m.