Package: tLOH 1.20.0

Michelle Webb

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

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).

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

tLOH_1.20.0.tar.gz
tLOH_1.20.0.zip(r-4.7)tLOH_1.20.0.zip(r-4.6)tLOH_1.20.0.zip(r-4.5)
tLOH_1.20.0.tgz(r-4.6-any)tLOH_1.20.0.tgz(r-4.5-any)
tLOH_1.20.0.tar.gz(r-4.7-any)tLOH_1.20.0.tar.gz(r-4.6-any)
tLOH_1.20.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
tLOH/json (API)

# Install 'tLOH' in R:
install.packages('tLOH', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/uscdtg/tloh/issues

Datasets:
  • humanGBMsampleAC - Imported dataset of a human glioblastoma spatial transcriptomics sample processed with tLOHImportData.
  • initialStartProbabilities - Imported dataset of sample start probabilities for hiddenMarkovAnalysis

On CRAN:

Conda:

copynumbervariationtranscriptionsnpgeneexpressiontranscriptomics

3.65 score 3 stars 4 scripts 318 downloads 23 exports 151 dependencies

Last updated from:d2ec0cce88 (on RELEASE_3_23). Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING237
linux-devel-x86_64ERROR490
source / vignettesOK392
linux-release-x86_64ERROR549
macos-release-arm64ERROR275
macos-oldrel-arm64ERROR363
windows-develERROR465
windows-releaseERROR395
windows-oldrelERROR446
wasm-releaseOK171

Exports:aggregateCHRPlotalleleFrequencyPlotdocumentErrorRegionshiddenMarkovAnalysismarginalLikelihoodM1marginalLikelihoodM2marginalM1CalcmarginalM2CalcBHETmarginalM2CalcBLOHmodePeakCalcprepareHMMdataframesregionAnalysisregionFinalizeremoveOutlierFromCalcrunHMM_1runHMM_2runHMM_3splitByChromosomesummarizeRegions1summarizeRegions2tLOHCalctLOHCalcUpdatetLOHDataImport

Dependencies:abindAnnotationDbiaskpassbestNormalizeBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebutchercachemcigarilloclassclicliprclockcodetoolscpp11crayoncurldata.tableDBIDelayedArraydepmixS4diagramdigestdoParalleldoRNGdplyrfarverfastmapforcatsforeachformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2globalsgluegowergridExtragtablehardhathmshttripredIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rLambertWlamWlatticelavalifecyclelistenvlobstrlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimenaniarnlmennetnormnortestnumDerivopensslparallellypillarpkgconfigplyrpngprettyunitsprodlimprogressprogressrpurrrR6RColorBrewerRcppRcppArmadilloRcppParallelRCurlreadrrecipesreshape2restfulrRhtslibrjsonrlangrngtoolsrpartRsamtoolsRsolnpRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraysparsevctrsSQUAREMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimechangetimeDatetruncnormtzdbUpSetRutf8VariantAnnotationvctrsviridisviridisLitevisdatvroomwithrXMLXVectoryaml

tLOH

Michelle Webb

Rendered fromtLOH_vignette.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-10-18
Started: 2021-05-03