使用 R 检索 GWAS 信息
I am trying to get specific disease-related information from the GWAS catalog. This can be done directly from the website via a spreadsheet download. But I was wondering if I could possibly do it programmatically in R. Any suggestions will be greatly appreciated.
Thanks.
Avoks
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查看函数 download.file() 和包 rcurl (http://cran.r-project.org/web/packages/RCurl/index.html) - 这应该可以满足您的需求
Checkout the function download.file() and the package rcurl (http://cran.r-project.org/web/packages/RCurl/index.html) - this should do what you are looking for
您必须先下载 .tsv 文件并手动编辑它们。
这是因为 GWAS 目录文件包含 HTML 符号，例如“Behçet 病”中的 §（定义特殊的第四个字母）。这些符号中的#将被R解释为行尾，因此你会收到一条错误消息，例如：
So you download it first, open in plain text编辑器中，自动将每个 # 替换为空字符，然后将其加载到 R 中：
read.table("gwas_catalog_v1.0-associations_e91_r2018-02-21.tsv",sep="\t",h=T,stringsAsFactors = F,quote="")You will have to download .tsv file(s) first and manually edit them.
This is because GWAS Catalog files contain HTML symbols, like § in "Behçet's disease" (defining that special fourth letter). The # in these symbols will be interpreted by R as an end of line, thus you will get an error message, e.g.:
So you downlad it first, open in plain text editor, automatically replace every # with empty character, and only then load it into R with:
read.table("gwas_catalog_v1.0-associations_e91_r2018-02-21.tsv",sep="\t",h=T,stringsAsFactors = F,quote="")