bmi_exp_dat_clumped<-read_exposure_data(filename = bmi,sep = ",",snp_col = "ID",p_col = "p",se_col = "SE",effect_allele_col = "alt",other_allele_col = "ref",clump = TRUE)
时间: 2023-06-27 15:01:20 浏览: 188
这行代码的作用是读取一个名为 "bmi" 的数据文件,其中包含SNP ID、p值、SE、效应等位基因和其它等位基因等信息,并进行数据聚类(clump),生成一个新的数据集 "bmi_exp_dat_clumped"。其中,参数 "sep" 表示数据文件中列之间的分隔符为逗号(","),"snp_col" 表示SNP ID所在的列,"p_col" 表示p值所在的列,"se_col" 表示SE所在的列,"effect_allele_col" 表示效应等位基因所在的列,"other_allele_col" 表示另一等位基因所在的列。
相关问题
exposure_dat <- ld_clump_local( + dat = df1, + clump_kb = 500, + clump_r2 = 0.2, + clump_p = 1e-5, + bfile = "D:/R-language/MR代码/课题组数据/g1000_eas", + plink_bin = "D:/R-language/R-4.2.2/library/plinkbinr/bin/plink_Windows.exe" + ) PLINK v1.90b6.10 64-bit (17 Jun 2019) www.cog-genomics.org/plink/1.9/ (C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to C:\Users\86131\AppData\Local\Temp\Rtmp8kX5Lf\file3e5474b5111.log. Options in effect: --bfile D:/R-language/MR����/����������/g1000_eas --clump C:\Users\86131\AppData\Local\Temp\Rtmp8kX5Lf\file3e5474b5111 --clump-kb 500 --clump-p1 1e-05 --clump-r2 0.2 --out C:\Users\86131\AppData\Local\Temp\Rtmp8kX5Lf\file3e5474b5111 14188 MB RAM detected; reserving 7094 MB for main workspace. Allocated 5320 MB successfully, after larger attempt(s) failed. Error: Failed to open D:/R-language/MR����/����������/g1000_eas.bed. Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'C:\Users\86131\AppData\Local\Temp\Rtmp8kX5Lf\file3e5474b5111.clumped': No such file or directory
It seems like there is an error in the code related to file paths. Specifically, the error message says that the program failed to open the file "D:/R-language/MR����/����������/g1000_eas.bed". This could be due to incorrect file path or missing file. Additionally, there is a warning message that says "cannot open file 'C:\Users\86131\AppData\Local\Temp\Rtmp8kX5Lf\file3e5474b5111.clumped': No such file or directory". This could be due to the program not finding the output file at the specified location.
In file(file, "rt") : 无法打开文件'C:\Users\hs\AppData\Local\Temp\Rtmpqmv0HW\file16fc53af1e4b.clumped': No such file or directory
这个错误提示是由于无法找到指定的文件路径所导致的。可能有以下几种原因:
1. 文件路径错误:请确保文件路径是正确的,包括文件名和文件所在的文件夹路径。
2. 文件不存在:请检查文件是否存在于指定的路径中。如果文件不存在,可以尝试重新下载或者检查文件名是否正确。
3. 权限问题:请确保你有足够的权限来访问该文件。如果你没有权限,可以尝试以管理员身份运行程序或者修改文件权限。
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