未从UCSC装载hg38的R上的GVIZ

Question

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3.1
> packageVersion("Gviz")
[1] '1.36.2'
> packageVersion("GenomicRanges")
[1] '1.44.0'

我正在尝试可视化一些在hg38上处理的ATAC数据。GVIZ不会加载hg38数据，提供的错误是：

> itrack <- IdeogramTrack(genome = "hg38", chromosome = "chr4")
Error in value[[3L]](cond) : 
  There doesn't seem to be any chromosome length data available for genome 'hg38' at UCSC or the service is temporarily down.
In addition: Warning message:
In value[[3L]](cond) :
  There doesn't seem to be any cytoband data available for genome 'hg38' at UCSC or the service is temporarily down. Trying to fetch the chromosome length data.

去年10月，我遇到了一个类似的问题，试图加载mm10基因组，我遵循了之前所有的建议。我使用以下方法更新Gviz和GenomicRanges包：

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("Gviz")
BiocManager::install("GenomicRanges")

我也更新了R。有人有什么建议吗？非常感谢你的帮助。

Answer 1

用以下方式更新软件包：

    if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
    remotes::install_github("ivanek/Gviz")

似乎修复了这个错误。