Supporting data for the MutSeqR package

Annette E. Dodge and Matthew J. Meier*

*matthew.meier@hc-sc.gc.ca

Abstract

Description of your vignette

Package

MutSeqRData 0.99.4

Contents

1 MutSeqRData

This data package provides supporting data for MutSeqR.

This package contain the following objects:

• Example import_mut_data
• Example import_mut_data using Custom column names
• Example import_vcf_data
• Example mutation data
• Example mutation data filtered
• Precalculated Depth at Base 6 Resolution
• Precalculated Depth at Base 12 Resolution
• Precalculated Depth at Base 96 Resolution
• Precalculated Depth at Base 192 Resolution

2 Installation

Install MutSeqRData from Bioconductor:

if (!require("BiocManager", quietly=TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install("MutSeqRData")

Or from Github:

if (!require("devtools", quietly = TRUE)) {
  install.packages("devtools")
}
devtools::install_github("EHSRB-BSRSE-Bioinformatics/MutSeqRData")

Load the package:

library(MutSeqRData)

3 Access Data from ExperimentHub

if (!require("BiocManager", quietly=TRUE)) {
  install.packages("BiocManager")
}
if (!require("ExperimentHubData", quietly = TRUE)) {
  BiocManager::install("ExperimentHubData")
}
library(ExperimentHub)
eh <- ExperimentHub()
query(eh, "MutSeqRData")
mutation_data <- eh[["access # here"]]

4 Session info

## R Under development (unstable) (2025-12-22 r89219)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.39.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.39       R6_2.6.1            bookdown_0.46      
##  [4] fastmap_1.2.0       xfun_0.55           cachem_1.1.0       
##  [7] knitr_1.51          htmltools_0.5.9     rmarkdown_2.30     
## [10] lifecycle_1.0.5     cli_3.6.5           sass_0.4.10        
## [13] jquerylib_0.1.4     compiler_4.6.0      tools_4.6.0        
## [16] evaluate_1.0.5      bslib_0.9.0         yaml_2.3.12        
## [19] otel_0.2.0          BiocManager_1.30.27 jsonlite_2.0.0     
## [22] rlang_1.1.7