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:
exampleData <- tLOHDataImport('../inst/extdata/Example.vcf')
# The VCF file in inst/extdata must be decompressed before running this command
load("../data/humanGBMsampleAC.rda")
df <- tLOHCalc(humanGBMsampleAC)
head(df)
## rsID CLUSTER TOTAL REF ALT CHR POS p(D|het) p(D|loh) p(het|D)
## 1 rs10001 8 1 0 1 chr19 7646335 0.5 0.5 0.5
## 2 rs10001 9 1 1 0 chr19 7646335 0.5 0.5 0.5
## 3 rs10001 2 1 1 0 chr19 7646335 0.5 0.5 0.5
## 4 rs10007201 8 1 1 0 chr4 100187175 0.5 0.5 0.5
## 5 rs10007201 3 1 1 0 chr4 100187175 0.5 0.5 0.5
## 6 rs10013040 1 1 1 0 chr4 177309998 0.5 0.5 0.5
## p(loh|D) bayesFactors inverseBayes LogBayesFactors LogInverseBayes
## 1 0.5 1 1 -5.551115e-16 6.661338e-16
## 2 0.5 1 1 -6.661338e-16 6.661338e-16
## 3 0.5 1 1 -6.661338e-16 6.661338e-16
## 4 0.5 1 1 -6.661338e-16 6.661338e-16
## 5 0.5 1 1 -6.661338e-16 6.661338e-16
## 6 0.5 1 1 -6.661338e-16 6.661338e-16
## Log10BayesFactors Log10InverseBayes AF CLUSTER_AF CHR_F
## 1 -2.410819e-16 2.892982e-16 1 9 19
## 2 -2.892982e-16 2.892982e-16 0 9 19
## 3 -2.892982e-16 2.892982e-16 0 2 19
## 4 -2.892982e-16 2.892982e-16 0 8 4
## 5 -2.892982e-16 2.892982e-16 0 3 4
## 6 -2.892982e-16 2.892982e-16 0 1 4
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
alleleFrequencyPlot(df, "Example")