input2PWcTalk: Example input data to pathway crosstalk analysis

In hui-sheen/MetaGSCA: Meta-analysis of Gene Set differential Co-expression Analysis

Example input data to pathway crosstalk analysis

Description

Data frame outputted from prior steps of multi-pathway meta-analysis in our pan-cancer case study

Usage

data(input2PWcTalk)

Format

A data frame with 330 observations across 14 variables. Each observation corresponds to a pathway.

• Number.of.Genes Number of Genes included in the pathway

• meta.p Meta-analysis summarized permutation p-value across 11 datasets

• bootstrap.p Median of Meta-analysis summarized bootstrap p-values across 11 datasets

• BRCA permutation p-value in Breast invasive carcinoma

• COAD permutation p-value in Colon adenocarcinoma

• HNSC permutation p-value in Head and Neck squamous cell carcinoma

• KIRC permutation p-value in Kidney renal clear cell carcinoma

• KIRP permutation p-value in Kidney renal papillary cell carcinoma

• LIHC permutation p-value in Liver hepatocellular carcinoma

• LUAD permutation p-value in Lung adenocarcinoma

• LUSC permutation p-value in Lung squamous cell carcinoma

• PRAD permutation p-value in Prostate adenocarcinoma

• STAD permutation p-value in Stomach adenocarcinoma

• THCA permutation p-value in Thyroid carcinoma

Details

We conducted a pan-cancer case study with 330 pathways containing at least 10 genes. Eleven cancer types from TCGA that had a minimum of 30 normal samples were included in the meta-analysis. This dataset is a data frame outputted from function MetaGSCA().

Author(s)

Yan Guo, Hui Yu

Examples

data(input2PWcTalk)
head(input2PWcTalk)
row.names(input2PWcTalk) # Names of 330 pathways

hui-sheen/MetaGSCA documentation built on April 9, 2022, 7:24 p.m.