NEWS.md

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

tLOH ChangeLog

Changes in version 1.5.6 + Minor fix to output column names - added one output column and renamed

Changes in version 1.5.5 + Minor updates to existing functions + Changed output column names for hiddenMarkovAnalysis function + Adjusted formatting throughout files

Changes in version 1.5.4 + Added new set of functions for an experimental workflow with documentation. + Updated functions.R, globals.R, data.R + Added new .rda file for an example in manual files + Updated DESCRIPTION and NAMESPACE + Updated the Acknowledgment section in the README to cite additional packages added to workflow

Changes in version 1.5.3 + Added documentation of function and synced repositories

Changes in version 1.5.2 + Added mode peak calculation function

Changes in version 1.5.1 + Updated version numbering to match Bioconductor standard + Updated DESCRIPTION file + Updated README file

Changes in version 0.99.10 (2021-05-05) + Replaced DelayedArray in DESCRIPTION imports field with MatrixGenerics, updated NAMESPACE + Updated R dependency to R (>= 4.0) + Updated tLOHDataImport and tLOHCalc functions

Changes in version 0.99.9 (2021-05-4) + Added humanGBMsampleAC.Rd file to man/ + Added RoxygenNote line to DESCRIPTION

Changes in version 0.99.8 (2021-05-4) + Added import(DelayedArray) to NAMESPACE, was previously already in DESCRIPTION imports field + Changed matrixStats rowRanges to DelayedArray rowRanges in functions.R + Removed import of matrixStats rowRanges from NAMESPACE + Adjusted formatting in humanGBMsampleAC field of R/data.R documentation

Changes in version 0.99.7 (2021-05-4) + Renamed the data/dataExample.rda to data/humanGBMsampleAC.rda, which is a set of pre-processed allele counts from a human glioblastoma sample analyzed with the 10X Genomics Visium Spatial Gene Expression platform

Changes in version 0.99.6 (2021-05-4) + Testing dependency fix + Fixed typos

Changes in version 0.99.5 (2021-05-3) + Added back in vignette + Added running examples to documentation + Modified required input format to be only a VCF. Future option will include pre-processed CollapsedVCF object as well

Changes in version 0.99.4 (2021-05-1) + Modified required input format from directory of pre-processed .csv files to a VCF or VariantAnnotation CollapsedVCF object containing columns for each cluster + Split the plotLOH function into two shorter functions: alleleFrequencyPlot() and aggregateCHRPlot + Removed filtering within tLOHCalc. Detailed information on filtering for next update. + Modified NAMESPACE file + Added VariantAnnotation and GenomicRanges to README acknowledgments and DESCRIPTION file + Removed inst/extdata/sampleData.tar.gz and replaced with Example.vcf + Temporarily removed running examples in documentation - will update in next patch + Temporarily removed vignette - will update in next patch

Changes in version 0.99.3 (2021-04-27) + Updated plotLOH.Rd to not run the code example

Changes in version 0.99.2 (2021-04-27) + Updated VignetteEngine to knitr::rmarkdown from knitr::knitr in tLOH.Rmd + Updated lines in tLOH.Rmd

Changes in version 0.99.1 (2021-04-27) + Removed LazyData: true from DESCRIPTION file + Updated Description field in the DESCRIPTION file + Consolidated Author and Maintainer fields to Authors@R field in DESCRIPTION file + Removed tracking of system files .DS_Store and tLOH.Rproj by adding to .gitignore + Removed data/exampleDF.rda and added df.rda to inst/extdata + Updated vignette to reflect .rda location and name change + Updated vignette text to be more informative and contain link to pre-processing steps + Added documentation on contents of inst.extdata/df.rda in the vignette + Reduced size of sample images and tar.gz in inst/extdata

Changes in version 0.99.0 (2021-04-22) + Initial Code Edits + Updated README, CITATION, and vignette

USCDTG/tLOH documentation built on Oct. 23, 2022, 8:05 p.m.