Overview

ChIPexoQualExample is an the accompanying example data package for ChIPexoQual. The data was built from the FoxA1 in mouse liver experiment published by (Serandour et al. 2013), by considering only the reads aligned to chr1. To load the package it is necessary to use:

library(ChIPexoQualExample, quietly = TRUE)

This package contains these aligned reads and an example run with ChIPexoQual:

## example raw files
list.files(system.file("extdata", package = "ChIPexoQualExample"))

## [1] "ChIPexo_carroll_FoxA1_mouse_rep1_chr1.bam"    
## [2] "ChIPexo_carroll_FoxA1_mouse_rep1_chr1.bam.bai"
## [3] "ChIPexo_carroll_FoxA1_mouse_rep2_chr1.bam"    
## [4] "ChIPexo_carroll_FoxA1_mouse_rep2_chr1.bam.bai"
## [5] "ChIPexo_carroll_FoxA1_mouse_rep3_chr1.bam"    
## [6] "ChIPexo_carroll_FoxA1_mouse_rep3_chr1.bam.bai"

SessionInfo

sessionInfo()

## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [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: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.40.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.39       R6_2.6.1            fastmap_1.2.0      
##  [4] xfun_0.61           maketools_1.3.2     cachem_1.1.0       
##  [7] knitr_1.52          htmltools_0.5.9     rmarkdown_2.32     
## [10] buildtools_1.0.0    lifecycle_1.0.5     cli_3.6.6          
## [13] sass_0.4.10         jquerylib_0.1.4     compiler_4.6.1     
## [16] sys_3.4.3           tools_4.6.1         evaluate_1.0.5     
## [19] bslib_0.12.0        yaml_2.3.12         BiocManager_1.30.27
## [22] jsonlite_2.0.0      rlang_1.3.0