Results/model/README.md

In shbrief/GenomicSuperSignaturePaper: Reproduce GenomicSuperSignature paper

Rmarkdowns

What_RAVindex_Is.Rmd

General characterization of RAVmodel. This vignette contains the code to make Supplementary Figure 9.

PCs_In_Clusters.Rmd

This vignette contains the code to plot Supplementary Figure 10. Distribution of PCs in different sized RAVs.

Characterize_GSEA.Rmd

Characterize GSEA annotation part of RAVmodel. This vignette contains the code to make Supplementary Figure 11. RAVs without enriched pathways.

LINC.Rmd

Investigate how long intergenic non-coding (LINC) genes affect GSEA annotation of RAVmodel.

Simulate_PCSSs.Rmd

Simulate 4,764 RAVs following the distribution pattern of the actual RAVindex and evaluate how likely to obtain PCSS-like RAVs from the random RAVs.

Top10PCs_RAVmodel.Rmd

Together with lowerPCsInClsuters.csv, this vignette explains how we decide the number of PCs to collect for RAVmodel building through the sensitivity test.

Data files

pcNumAll.tsv

The significant number of PCs calculated through the elbow method. Actual calculation was done using PLIER::num.pc with modification. The script is available in PC_selection.Rmd

RAVs_with_topPCs.tsv

A table containing RAVs that have more than two top PCs (PC1/2/3) from the same study. This table doesn't contain all the PCs in the cluster, but only subset the PCs from the same study. The script is available What_RAVIndex_Is.Rmd

lowerPCsInClsuters.csv

A table summarize the frequency of lower PCs (PC11-20) in the different sized clusters. There are three columns: clusterSize, totalPCs (the total number of PCs contributing to the given size of cluster), and lowerPCs (the total number of PC11-20 in the given size of cluster). From PCs_In_Clusters.Rmd.

Top10PCs_RAVmodel.csv.gz

A matrix containing Pearson correlation coefficient between 2,382 RAVs from RAVmodel_10 (RAVmodel constructed from top 10 PCs) and 4,764 RAVs from RAVmodel_20 (RAVmodel constructed from top 20 PCs).

R Scripts

LINC.R

Script to build a RAVmodel without LINC genes.

listOfRAVmodels.R

Combine tsv files downloaded from Google Sheet and make availableRAVmodel.csv for GenomicSuperSignature package.

pathwayCoverage.R

Function to calculate pathway coverage

shbrief/GenomicSuperSignaturePaper documentation built on Aug. 2, 2022, 2:04 p.m.