Why in R string entries do not get read into the data.frame?

Question

I have a data.tsv file (tabs separate entries). The full file can be found here.

The entries in the file look like this:

">173D:C"   "TVPGVXTVPGV"   "CCSCCCCCCCC"
">173D:D"   "TVPGVXTVPGV"   "CCCCCCCCSCC"
">185D:A"   "SAXVSAXV"  "CCBCCCBC"
">1A0M:B"   "GCCSDPRCNMNNPDYCX" "CCTTSHHHHHTCTTTCC"
">1A0M:A"   "GCCSDPRCNMNNPDYCX" "CGGGSHHHHHHCTTTCC"
">1A0N:A"   "PPRPLPVAPGSSKT"    "CCCCCCCCSTTCCC"

I am trying to read string entries into the data frame (into a matrix containing 3 columns):

data = data.frame(read.csv(file = './data.tsv', header = FALSE, sep = '\t'))

but only the first column is read. All other columns are empty.

I also tried different commands, such as

data = read.csv(file = './data.tsv', header = FALSE, sep = '\t')
data = read.csv(file = './data.tsv', sep = '\t')
data = data.frame(read.csv(file = './data.tsv'))

but without success. Can someone foresee why the input does not get read successfully?

You don't need the data frame, `read.csv` returns that already. Use `read.table` for tab separated data. Check that you really have tabs in your data, not multiple spaces. — , May 28 '18 at 13:06

score 2 · Answer 1 · answered May 28 '18 at 11:56

Using the file defined reproducibly in the Note at the end this works:

DF <- read.table("myfile.dat", as.is = TRUE)

gives:

> DF
       V1                V2                V3
1 >173D:C       TVPGVXTVPGV       CCSCCCCCCCC
2 >173D:D       TVPGVXTVPGV       CCCCCCCCSCC
3 >185D:A          SAXVSAXV          CCBCCCBC
4 >1A0M:B GCCSDPRCNMNNPDYCX CCTTSHHHHHTCTTTCC
5 >1A0M:A GCCSDPRCNMNNPDYCX CGGGSHHHHHHCTTTCC
6 >1A0N:A    PPRPLPVAPGSSKT    CCCCCCCCSTTCCC

Note

Lines <- '">173D:C"   "TVPGVXTVPGV"   "CCSCCCCCCCC"
">173D:D"   "TVPGVXTVPGV"   "CCCCCCCCSCC"
">185D:A"   "SAXVSAXV"  "CCBCCCBC"
">1A0M:B"   "GCCSDPRCNMNNPDYCX" "CCTTSHHHHHTCTTTCC"
">1A0M:A"   "GCCSDPRCNMNNPDYCX" "CGGGSHHHHHHCTTTCC"
">1A0N:A"   "PPRPLPVAPGSSKT"    "CCCCCCCCSTTCCC"'
writeLines(Lines, "myfile.dat")

user387832 · Accepted Answer · 2018-05-28T12:01:42.033

1

Use sep=''

data = read.csv(file = './data.tsv', header = FALSE, sep = '')

See this answer.

edited May 28 '18 at 12:01

answered May 28 '18 at 11:56

user387832

503
3
8

`read.csv` produces a data.frame as its output. there is no need for `data.frame()` – G5W May 28 '18 at 11:59
I tried this, but the result is the same, I also removed `data.frame()` – mercury0114 May 28 '18 at 12:01
1

This works on my machine with the data you've given so I'm not sure how else to help. Maybe try G. Grothendieck's answer. – user387832 May 28 '18 at 12:03
Actually your method works, just print(data) does not properly print the data, thanks. – mercury0114 May 28 '18 at 13:45

Why in R string entries do not get read into the data.frame?

2 Answers2

Note