DOI: 10.18129/B9.bioc.tLOH  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see tLOH.

Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

Bioconductor version: 3.16

tLOH, or transcriptomicsLOH, assesses evidence for loss of heterozygosity (LOH) in pre-processed spatial transcriptomics data. This tool requires spatial transcriptomics cluster and allele count information at likely heterozygous single-nucleotide polymorphism (SNP) positions in VCF format. Bayes factors are calculated at each SNP to determine likelihood of potential loss of heterozygosity event. Two plotting functions are included to visualize allele fraction and aggregated Bayes factor per chromosome. Data generated with the 10X Genomics Visium Spatial Gene Expression platform must be pre-processed to obtain an individual sample VCF with columns for each cluster. Required fields are allele depth (AD) with counts for reference/alternative alleles and read depth (DP).

Author: Michelle Webb [cre, aut], David Craig [aut]

Maintainer: Michelle Webb <michelgw at>

Citation (from within R, enter citation("tLOH")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script tLOH
PDF   Reference Manual
Text   NEWS


biocViews CopyNumberVariation, GeneExpression, SNP, Software, Transcription, Transcriptomics
Version 1.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License MIT + file LICENSE
Depends R (>= 4.2)
Imports scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics, bestNormalize, depmixS4, naniar, stringr
Suggests knitr, rmarkdown
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package tLOH_1.6.0.tar.gz
Windows Binary
macOS Binary (x86_64) tLOH_1.6.0.tgz
macOS Binary (arm64) tLOH_1.6.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: