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brcasurv

Age-adjusted survival associations of gene signatures in TCGA/METABRIC/SCANB

https://github.com/montilab/brcasurv

Science Score: 44.0%

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Age-adjusted survival associations of gene signatures in TCGA/METABRIC/SCANB

Basic Info
  • Host: GitHub
  • Owner: montilab
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 25.4 KB
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  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 1 year ago · Last pushed 6 months ago
Metadata Files
Readme Citation

README.md

Lifecycle: experimental <!-- badges: end -->

brcasurv

Helper functions to estimate the survival associations of user-provided gene signatures in TCGA/METABRIC/SCANB.

Installation:

devtools::install_github("montilab/brcasurv")

Example Usage:

Given a named list of gene sets e.g. list(GS1 = c("gene1", "gene2", "gene3")) one can score each sample in TCGA/METABRIC with gsva_data and use gsva_cox_fit to fit coxph models.

``` gsvadata <- gsvadata(sigslist = sigslist, brcadata = "TCGA", # Or "METABRIC/SCANB" adjustprolif = TRUE, adjust_inflam = TRUE)

gsvacoxfits <- gsvacoxfit(gsvadata, brcadata = "TCGA", # Or "METABRIC/SCANB" adjustage = TRUE, adjustprolif = TRUE, adjust_inflam = TRUE) ```

Plotting:

Example of plotting code that uses survminer::ggadjustedcurves to plot results from the cox models. Since gsva scores of a geneset are continuous, we need to first make the geneset scores into a categorical variable and define a new cox model. gsva_data$sig <- t(exprs(gsva_data[“sig_name”,]) gsva_sig_median <- median(gsva_data$sig) gsva_data$stat <- with(gsva_data, ifelse(gsva_data$sig < gsva_sig_median, 0, 1)) cox_fit <- coxph(Surv(as.numeric(time_5), vital_status_5) ~ age_at_index + stat, data = pData(gsva_data))

Now we can plot the two adjusted survival curves. ``` if (!require("survminer", quietly = TRUE)) { install.packages("survminer") }

Replace parameters with relevant data.

ggadjustedcurves(fit = {coxfit}, data = {pData(gsvadata)}, method = "conditional", variable = {signature_name}, xlab = "Days", ylab = "Survival Probability", pval = TRUE, title = "TCGA/METABRIC/SCANB age-adjusted cox model" ) ```

Owner

  • Name: Monti Lab
  • Login: montilab
  • Kind: organization
  • Email: montilab@bu.edu

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Chen"
  given-names: "Andrew"
  orcid: "https://orcid.org/0000-0002-8508-0227"
title: "brcasurv"
version: 1.0.0
date-released: 2025-01-15
url: "https://github.com/montilab/brcasurv"

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