Contents

{r style, echo = FALSE, results = 'asis'} BiocStyle::markdown()

1 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"

2 SessionInfo

sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## 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       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.26.0
## 
## loaded via a namespace (and not attached):
##  [1] bookdown_0.29       digest_0.6.30       R6_2.5.1           
##  [4] jsonlite_1.8.3      magrittr_2.0.3      evaluate_0.17      
##  [7] stringi_1.7.8       cachem_1.0.6        rlang_1.0.6        
## [10] cli_3.4.1           jquerylib_0.1.4     bslib_0.4.0        
## [13] rmarkdown_2.17      tools_4.2.1         stringr_1.4.1      
## [16] xfun_0.34           yaml_2.3.6          fastmap_1.1.0      
## [19] compiler_4.2.1      BiocManager_1.30.19 htmltools_0.5.3    
## [22] knitr_1.40          sass_0.4.2

References

Serandour, Aurelien, Brown Gordon, Joshua Cohen, and Jason Carroll. 2013. “Development of and Illumina-Based ChIP-Exonuclease Method Provides Insight into FoxA1-DNA Binding Properties.” Genome Biology.