[BUG]: format_data() Error: j（在 [...] 中的第二个参数）是单一符号，但未找到列名 'i'

[Carnivalera]

Describe the bug (required)

When using the function format_data(), an error alert emerged.

Describe the current behaviour you observe (required)

错误: j（在 [...] 中的第二个参数）是单一符号，但未找到列名 'i'。如果你打算在调用环境中使用变量选择列，请尝试 DT[, ..i]。.. 前缀表示上一级，类似于文件系统路径。

Describe the behaviour you expect (required)

R code to reproduce the issue (required)

BMI_OUT<-TwoSampleMR::format_data(dat = BMI, type = "outcome", snps = CAD$SNP, header = TRUE, snp_col = "variant_id", beta_col = "beta", se_col = "standard_error", effect_allele_col = "effect_allele", other_allele_col = "other_allele", pval_col = "p_value")

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System information

Please provide details of your operating system and R version

Additional context

Add any other context about the problem here

[Diekunstderfug]

Surely when I want to user format_dat, I check my data for manys time, but the error repeatly occurs. Finally I read the source codes, It seems that the variant "i" is not state properly. Please fix it if you have time, thanks!

[filmchen]

Have you resolved the issue? I have met the same problem, it would be appreciated if there is any suggestion!

[filmchen]

Editing the function TwoSampleMR::data.table(), instead "dat <- dat[, i]" with "dat <- dat[, ..i]",which can solve this problem.

[JPRAH-MORMONT]

编辑函数 TwoSampleMR：:d ata.table（），改为“dat <- dat[， i]”和“dat <- dat[， ..i]“，可以解决这个问题。
I have met the same problem
Thanks for your answer, however I can't understand the meaning.
It would be appreciated if there is more detailed answer or the code

[nadineparker]

I also had this issue when updating the TwoSampleMR package. An old script that worked 6 months ago (likely with v5.7) no longer works now (with v5.11). I assume something broke with one of the recent version updates.

[remlapmot]

The opengwas API has been updated. So you need to update your version of the ieugwasr package and obtain a new token.

The package can be updated with the following code.

For Windows and Mac users

install.packages("ieugwasr", repos = c("https://mrcieu.r-universe.dev", "https://cran.r-project.org"))

For Ubuntu Jammy Jellyfish users

# Installation code for Ubuntu Jammy Jellyfish users running R in the Terminal
options(HTTPUserAgent = sprintf(
  "R/%s R (%s)",
  getRversion(),
  paste(getRversion(),
        R.version["platform"],
        R.version["arch"],
        R.version["os"])
))

install.packages(
  'ieugwasr',
  repos = c(
    'https://mrcieu.r-universe.dev/bin/linux/jammy/4.3/',
    'https://packagemanager.posit.co/cran/__linux__/jammy/latest',
    'https://cloud.r-project.org'
  )
)

Or

install.packages('remotes')
remotes::install_github('MRCIEU/ieugwasr')

[remlapmot]

Please see MRCIEU/ieugwasr#65 (comment) for the instructions about the token.