如何确定txt文件中使用的delim类型？

Question

Here is my sample data: https://github.com/Patricklv/Txt-file

I tried to load the data using the following code:

library(tidyverse)
data <- read_delim("<PATH>\\pgc.cross.SCZ17.2013-05.txt", delim = " ")
head(data)

This returns the following results:

# A tibble: 6 × 12
  snpid    hg18chr bp    a1    a2    or    se    pval  info  ngt   CEUaf
  <chr>    <lgl>   <lgl> <lgl> <lgl> <lgl> <lgl> <lgl> <lgl> <lgl> <lgl>
1 "rs3131… NA      NA    NA    NA    NA    NA    NA    NA    NA    NA   
2 "rs3131… NA      NA    NA    NA    NA    NA    NA    NA    NA    NA   
3 "rs3131… NA      NA    NA    NA    NA    NA    NA    NA    NA    NA   
4 "rs1048… NA      NA    NA    NA    NA    NA    NA    NA    NA    NA   
5 "rs1256… NA      NA    NA    NA    NA    NA    NA    NA    NA    NA   
6 "rs4040… NA      NA    NA    NA    NA    NA    NA    NA    NA    NA   
# … with 1 more variable: ...12 <lgl>
# ℹ Use `colnames()` to see all variable names

I also tried:

data <- read_delim("<PATH>\\pgc.cross.SCZ17.2013-05.txt", delim = "\t")
head(data)

This returns:

# A tibble: 6 × 1
  `snpid hg18chr bp a1 a2 or se pval info ngt CEUaf `                   
  <chr>                                                                 
1 "rs3131972\t1\t742584\tA\tG\t1\t0.0966\t0.9991\t0.702\t0\t0.16055"    
2 "rs3131969\t1\t744045\tA\tG\t1\t0.0925\t0.9974\t0.938\t0\t0.133028"   
3 "rs3131967\t1\t744197\tT\tC\t1.001\t0.0991\t0.9928\t0.866\t0\t."      
4 "rs1048488\t1\t750775\tT\tC\t0.9999\t0.0966\t0.9991\t0.702\t0\t0.8364…
5 "rs12562034\t1\t758311\tA\tG\t1.025\t0.0843\t0.7716\t0.988\t0\t0.0925…
6 "rs4040617\t1\t769185\tA\tG\t0.9993\t0.092\t0.994\t0.979\t0\t0.87156"

However, when I open the file using Sublime Text, here is what I see:

I want to know how should I import this txt file so that it will appear as it shows in Sublime Text

Answer 1

Try read.table . No packages are used.

u <- "https://raw.githubusercontent.com/Patricklv/Txt-file/main/pgc.cross.SCZ17.2013-05.txt"
dat <- read.table(u, header = TRUE, na.strings = ".")

str(dat)

giving

'data.frame':   12 obs. of  11 variables:
 $ snpid  : chr  "rs3131972" "rs3131969" "rs3131967" "rs1048488" ...
 $ hg18chr: int  1 1 1 1 1 1 1 1 1 1 ...
 $ bp     : int  742584 744045 744197 750775 758311 769185 828418 836671 843817 844113 ...
 $ a1     : chr  "A" "A" "T" "T" ...
 $ a2     : chr  "G" "G" "C" "C" ...
 $ or     : num  1 1 1 1 1.02 ...
 $ se     : num  0.0966 0.0925 0.0991 0.0966 0.0843 ...
 $ pval   : num  0.999 0.997 0.993 0.999 0.772 ...
 $ info   : num  0.702 0.938 0.866 0.702 0.988 0.979 0.439 1.02 0.383 0.251 ...
 $ ngt    : int  0 0 0 0 0 0 0 0 0 0 ...
 $ CEUaf  : num  0.1605 0.133 NA 0.8364 0.0926 ...