In USCDTG/tLOH: Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

knitr::opts_chunk$set(echo = TRUE)
library('tLOH')
library('purrr')
library('dplyr')
library('GenomicRanges')
library('VariantAnnotation')

v1.5.6

tLOH: Assessment of evidence for loss of heterozygosity in spatial transcriptomics pre-processed data using Bayes factor calculations.

This tool requires data produced with the 10X Genomics Visium Spatial Gene Expression platform and processed to obtain a VCF with per-cluster allele count information at heterozygous SNP positions. The purpose of this R package is to perform Bayes calculations on the data from the VCF and plot the results. Examples of how to run this tool are below:

1. tLOHDataImport() is a function to import data for use by tLOHCalc(). The input is a VCF file, an example can be found in the inst/extdata folder.

exampleData <- tLOHDataImport('../inst/extdata/Example.vcf')
# The VCF file in inst/extdata must be decompressed before running this command

1. tLOHCalc() is the main calculation function. It requires the output directory from tLOHDataImport().

load("../data/humanGBMsampleAC.rda")
df <- tLOHCalc(humanGBMsampleAC)
head(df)

The column descriptions for the output dataframe are as follows - CHR: chromosome POS: position REF: reference allele counts ALT: alternative allele counts TOTAL: total counts p(D|het): probability of data given heterozygous event p(D|loh): probability of data given loh event p(het|D): probability of data given heterozygous event divided by the addition of p(D|het) and p(D|loh) p(loh|D): probability of data given loh event divided by the addition of p(D|het) and p(D|loh) bayesFactors: Bayes factor value K inverseBayes: 1/K LogBayesFactors: log of Bayes factor K LogInverseBayes: log of 1/K Log10BayesFactors: log 10 of Bayes factor K Log10InverseBayes: log 10 of 1/K AF: allele fraction Cluster: cluster number Cluster_AF: cluster + AF for plotting y axis CHR_F: chromosome factor

1. tLOH has two plotting functions, alleleFrequencyPlot() and aggregateCHRPlot(). Both require the output dataframe from running tLOHCalc, and a sample name for the plot title. Example images of these plots are available in inst/extdata.

alleleFrequencyPlot(df, "Example")

aggregateCHRPlot(df, "Example")

USCDTG/tLOH documentation built on Jan. 6, 2025, 11:12 p.m.