CODEWITHSUNDEEP
r
Vincent
Vincent

Reputation: 13

Use a file as input in a R function

I am totally new to R and I'm trying to run a function from a specific package : getId.

It works like this :

data<-getId(c('Pestivirus A','Bos taurus','Homo'),taxaNames)

However I have a lot of different data like 'Pestivirus A'. I have all of the inputs in a tsv files like this :

Pestivirus A
Bos taurus
...

Is there a clean easy way to put all these 7000 inputs ?

So far I converted my results in a .txt file like this :

'Pestivirus A','Bos taurus','Homo'...

And I have tried to import this file like this :

> species <- read.csv("C:/Users/vdoinel/Desktop/5_species.txt")

But I get an error " Error in file(file, "rt") : impossible d'ouvrir la connexion" and "No such file or directory". But anyway even if it has worked I don't know what to do after.

Upvotes: 0

Views: 337

Answers (2)

cdalitz
cdalitz

Reputation: 1277

Here are some hints:

  • read.csv returns a "data.frame", which is a two dimensional data structure with rows and cols. Let us call this data.frme "x". Make sure to read the file with header=FALSE, because you do not have colnames.
  • all your items are in one row (the first one), so you can read them with items <- x[1,]
  • you can loop over your items with for (item in items) {...}

The details should be looked up in your preferred R reference book/site.

Upvotes: 1

David
David

Reputation: 10162

While there is nothing wrong with @cdalitz answer, I personally prefer the tidyverse, which allows you to do the same things in a (imho) nicer way.

In your case:

library(tidyverse)

# list all .txt files, the $ signals end of text
files <- list.files(pattern = ".txt$")

# map the files to the function read_tsv (reads in the data); 
# assign the filenames as names to the list
data <- map(files, read_tsv) %>% set_names(files)

# data is now a list containing the data of the files;
# each slot holds data from one file

# combine the list to a single dataset/data.frame with a new variable called "file" containing the file name
data_all <- bind_rows(data, .id = "file")

Upvotes: 0

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