Package: tLOH 1.15.0

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_1.15.0.tar.gz
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tLOH.pdf |tLOH.html✨
tLOH/json (API)

# Install 'tLOH' in R:

install.packages('tLOH', repos = c('https://bioc.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 BioConductor:tLOH-1.15.0(bioc 3.21)tLOH-1.14.0(bioc 3.20)

copynumbervariation transcription snp geneexpression transcriptomics

4.48 score 3 stars 4 scripts 180 downloads 23 exports 155 dependencies

Last updated 4 months agofrom:fba6f99732. Checks:3 OK, 5 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 20 2025
R-4.5-win	NOTE	Feb 20 2025
R-4.5-mac	NOTE	Feb 20 2025
R-4.5-linux	NOTE	Feb 20 2025
R-4.4-win	NOTE	Feb 20 2025
R-4.4-mac	NOTE	Feb 20 2025
R-4.3-win	OK	Feb 20 2025
R-4.3-mac	OK	Feb 20 2025

Exports:aggregateCHRPlot alleleFrequencyPlot documentErrorRegions hiddenMarkovAnalysis marginalLikelihoodM1 marginalLikelihoodM2 marginalM1Calc marginalM2CalcBHET marginalM2CalcBLOH modePeakCalc prepareHMMdataframes regionAnalysis regionFinalize removeOutlierFromCalc runHMM_1 runHMM_2 runHMM_3 splitByChromosome summarizeRegions1 summarizeRegions2 tLOHCalc tLOHCalcUpdate tLOHDataImport

Dependencies:abind AnnotationDbi askpass bestNormalize BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome butcher cachem class cli clipr clock codetools colorspace cpp11 crayon curl data.table DBI DelayedArray depmixS4 diagram digest doParallel doRNG dplyr fansi farver fastmap forcats foreach formatR futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 globals glue gower gridExtra gtable hardhat hms httr ipred IRanges isoband iterators jsonlite KEGGREST KernSmooth labeling lambda.r LambertW lamW lattice lava lifecycle listenv lobstr lubridate magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell naniar nlme nnet norm nortest numDeriv openssl parallelly pillar pkgconfig plogr plyr png prettyunits prodlim progress progressr purrr R6 RColorBrewer Rcpp RcppParallel RCurl readr recipes reshape2 restfulr Rhtslib rjson rlang rngtools rpart Rsamtools Rsolnp RSQLite rtracklayer S4Arrays S4Vectors scales shape snow SparseArray sparsevctrs SQUAREM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange timeDate truncnorm tzdb UCSC.utils UpSetR utf8 VariantAnnotation vctrs viridis viridisLite visdat vroom withr XML XVector yaml

tLOH

Michelle Webb

Rendered fromtLOH_vignette.Rmdusingknitr::rmarkdownon Feb 20 2025.

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

Help page	Topics
Visualization of data output from the tLOHCalc function, aggregated per chromosome	aggregateCHRPlot
Visualization of data output from the tLOHCalc function	alleleFrequencyPlot
Identification of Errors	documentErrorRegions
Run Multi-Step HMM Analysis on tLOHCalcUpdate output	hiddenMarkovAnalysis
Imported dataset of a human glioblastoma spatial transcriptomics sample processed with tLOHImportData.	humanGBMsampleAC
Imported dataset of sample start probabilities for hiddenMarkovAnalysis	initialStartProbabilities
Marginal M1 Calculation	marginalLikelihoodM1
Marginal M2 Calculation	marginalLikelihoodM2
Calculate marginal of Model 1	marginalM1Calc
Calculation of marginal M2 het	marginalM2CalcBHET
Marginal M2 Calculation	marginalM2CalcBLOH
Calculation of mode peak	modePeakCalc
Prepare dataframes for HMM analysis	prepareHMMdataframes
Summary of HMM Regions	regionAnalysis
Summary of HMM Regions	regionFinalize
Removes outliers	cols dataframe newValue removeOutlierFromCalc rows
Step 1 of HMM process	runHMM_1
Step 2 of HMM process	runHMM_2
Step 3 of HMM process	runHMM_3
Split dataframe into individual chromosome dataframes	splitByChromosome
Step 1 of region summary	summarizeRegions1
Step 2 of region summary	summarizeRegions2
Assement of evidence for LOH in clusters from spatial transcriptomics data	tLOHCalc
Assement of evidence for LOH in clusters from spatial transcriptomics allele count data	tLOHCalcUpdate
Import VCF for tLOHCalc	tLOHDataImport

Package: tLOH 1.15.0

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

tLOH

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