harrig12 / TrackSigFreq-dev

Morris Lab, University of Toronto. Signature Trajectories of cancer evolution (TrackSig R package)

TrackSig R package (dev)

Morris Lab, University of Toronto. R package for TrackSig, TrackSigFreq.

To cite, please see https://www.biorxiv.org/content/10.1101/260471v3

Vignette

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Dependencies

R >= 3.3.3

This package imports the following other R packages:

• reshape2 >= 1.4.3 (CRAN)
• ggplot2 >= 3.2.0 (CRAN)
• NMF >= 0.21.0 (CRAN)
• assertthat >= 0.2.1 (CRAN)
• BSgenome.Hsapiens.UCSC.hg19 >= 1.4.0 (Bioconductor)
• GenomicRanges >= 1.26.4 (Bioconductor)
• Biostrings >= 2.42.1 (Bioconductor)
• SummarizedExperiment >= 1.4.0 (Bioconductor)
• VariantAnnotation >= 1.20.3 (Bioconductor)
• grid >= 3.3.3 (CRAN)
• progress >= 1.2.2 (CRAN)

Load the package in R

devtools::install_github("harrig12/TrackSigFreq-dev")

Demo

Using the example data provided in extdata/, the following code will plot the signature trajectory, and return the fitted mixture of signatures for each bin, the bins where changepoints were detected, and the ggplot object.

1. First, restrict the list of signatures to fit exposure for. This is recommended for improving speed by making the model smaller. Here, we choose a threshold of 5%, meaning that signatures with exposure under this across all timepoints will not be fit.

library(TrackSig)
library(ggplot2)

vcfFile = system.file(package = "TrackSig", "extdata/Example.vcf")
cnaFile = system.file(package = "TrackSig", "extdata/Example_cna.txt")
purity = 1

detectedSigs <- detectActiveSignatures(vcfFile = vcfFile, cnaFile = cnaFile,
                                       purity = purity, threshold = 0.05)

2. Next, we compute the trajectory for all timepoints.

set.seed(1224)

# a warning will appear about not matching the refrence genome, this is because the
# example vcf file is generated by sampling random nucleotides, not real mutations. 
traj <- TrackSig(sampleID = "example", activeInSample = detectedSigs,
                 vcfFile = vcfFile, cnaFile = cnaFile, purity = purity)

3. Plot the trajectory. If we plot with non-linear x-axis, then we can use the funciton addPhiHist()

plotTrajectory(traj, linearX = T) + labs(title = "Example trajectory with linear x-axis")

nonLinPlot <- plotTrajectory(traj, linearX = F) + labs(title = "Example trajectory with non-linear x-axis")
addPhiHist(traj, nonLinPlot)

Note

Some users may have plotting issues with TrackSig if ggplot2 is not explicitly loaded with library(ggplot2). We are experiencing a bug that has been previously described for ggplot2.