CODEWITHSUNDEEP
rimportread.tablereadr
Andrew Voronkov
Andrew Voronkov

Reputation: 511

How to import a .tsv file

I need to read a table that is a .tsv file in R.

enter image description here

test <- read.table(file='drug_info.tsv')
# Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
#   line 1 did not have 10 elements
test <- read.table(file='drug_info.tsv', )
# Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
#   line 1 did not have 10 elements
scan("drug_info.tsv")
# Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
#   scan() expected 'a real', got 'ChallengeName'
scan(file = "drug_info.tsv")
# Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
#   scan() expected 'a real', got 'ChallengeName'

How should I read it?

Upvotes: 41

Views: 168168

Answers (6)

woutcault
woutcault

Reputation: 51

You need to include fill = TRUE. 

test <- read.table(file='drug_info.tsv', sep = '\t', header = TRUE, fill = TRUE)

Upvotes: 5

Sam Old
Sam Old

Reputation: 152

You can treat the data like a csv, and specify tab delimination.

read.csv("drug_info.tsv", sep = "\t")

Upvotes: 14

千木郷
千木郷

Reputation: 1821

utils::read.delim() is most commonly used in such case if you don't want to install other library. The sample code could be something like:

test <- read.delim(file='drug_info.tsv')

or much more friendly io functions could be available from readr library, where a read_tsv named function is available directly:

test <- readr::read_tsv('drug_info.tsv')

Upvotes: 6

TBhavnani
TBhavnani

Reputation: 771

Using fread from the package data.table will read the data and will skip the error you are getting using read.table.

require(data.table)

data<-as.data.frame(fread("drug_info.tsv"))

Upvotes: 16

Robert Hijmans
Robert Hijmans

Reputation: 47591

Assuming that only the first line does not have the right number of elements, and that this is the column names line. Skip the first line:

 d <- read.table('drug_info.tsv', skip=1)

Now read it

 first <- readLines('drug_info.tsv', n=1)

Inspect it, fix it such that its number of elements matches d and then

 colnames(d) <- first

If that does not work, you can do

 x <- readLines('drug_info.tsv')

and diagnostics like this:

 sapply(x, length)

Upvotes: 5

Robert
Robert

Reputation: 2231

This should do it:

read.table(file = 'drug_info.tsv', sep = '\t', header = TRUE)

Upvotes: 47

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