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.

相关问题

asm_exp_dat <- extract_instruments(outcomes = 'ebi-a-GCST90014325') asm <- extract_instruments(outcomes = 'ebi-a-GCST90014325', clump = TRUE, r2 = 0.001, kb = 10000, access_token = NULL) #如果想要调整P值 asm_1 <- extract_instruments(outcomes = 'ebi-a-GCST90014325', p1 = 5e-08, clump = TRUE, r2 = 0.001, kb = 10000, access_token = NULL)bca_out <- extract_outcome_data( snps=data$SNP, outcomes='ieu-a-1127', proxies = FALSE, maf_threshold = 0.01, access_token = NULL ) mydata <- harmonise_data( exposure_dat=asm_1, outcome_dat=bca_out, action= 3 )Error in data$SNP : object of type 'closure' is not subsettable >我该如何修改？正确的代码是？

根据代码，你是想从 `data` 中提取 `SNP` 列，但是出现了错误。这个错误的原因可能是 `data` 不是一个数据框或数据表，而是一个函数。因此，你需要先执行 `data()` 函数，将数据加载到内存中，然后再提取 `SNP` 列。

修改后的代码如下：

data() # 加载数据
bca_out <- extract_outcome_data(
  snps = mydata$SNP, # 提取 mydata 数据框的 SNP 列
  outcomes = 'ieu-a-1127',
  proxies = FALSE,
  maf_threshold = 0.01,
  access_token = NULL
)

另外，你在上面的代码中使用了 `asm_1` 数据框，但是它没有在代码中定义。如果需要使用 `asm_1` 数据框，请先定义并赋值。

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)

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。