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)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()## R version 3.6.1 (2019-07-05)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.10-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.10-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 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] ChIPexoQualExample_1.10.0 BiocStyle_2.14.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.2 bookdown_0.14 digest_0.6.22
## [4] magrittr_1.5 evaluate_0.14 rlang_0.4.1
## [7] stringi_1.4.3 rmarkdown_1.16 tools_3.6.1
## [10] stringr_1.4.0 xfun_0.10 yaml_2.2.0
## [13] compiler_3.6.1 BiocManager_1.30.9 htmltools_0.4.0
## [16] knitr_1.25Serandour, 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.