# Input / Output

We will learn how to:

* Read in a file

* Write out a file

* Save a graph in a file (Module 3)

## On vectors

* Read a file as a vector with the **scan** function

```{r, eval=F}

# Read in file

scan(file="file.txt")

# Save in object

k <- scan(file="file.txt")

```

By default, scans "double" (numeric) elements: it fails if the input contains characters.<br>

If non-numeric, you need to specify the type of data contained in the file:

```{r, eval=F}

# specify the type of data to scan

scan(file="file.txt",

what="character")

scan(file="~/file.txt",

what="character")

```

Regarding paths of files:<br>

If the file is not in the current directory, you can provide a full or relative path. For example, if located in the home directory, read it as:

```{r, eval=F}

scan(file="~/file.txt",

what="character")

```

* Write the content of a vector in a file:

```{r, eval=F}

# create a vector

mygenes <- c("SMAD4", "DKK1", "ASXL3", "ERG", "CKLF", "TIAM1", "VHL", "BTD", "EMP1", "MALL", "PAX3")

# write in a file

write(x=mygenes,

file="gene_list.txt")

```

Regarding paths of files:<br>

When you write a file, you can also specify a full or relative path:

```{r, eval=F}

# Write to home directory

write(x=mygenes,

file="~/gene_list.txt")

# Write to one directory up

write(x=mygenes,

file="../gene_list.txt")

```

## On data frames or matrices

* Read in a file into a data frame with the **read.table** function:

```{r, eval=F}

a <- read.table(file="file.txt")

```

You can convert it as a matrix, if needed, with:

```{r, eval=F}

a <- as.matrix(read.table(file="file.txt"))

```

Useful arguments:

<a href="https://sbcrg.github.io/CRG_RIntroduction/images/readtable.png"><img src="images/readtable.png" width="550/"></a>

* Write a data frame or matrix to a file:

```{r, eval=F}

write.table(x=a,

file="file.txt")

```

Useful arguments:

<a href="https://sbcrg.github.io/CRG_RIntroduction/images/readtable.png"><img src="images/writetable.png" width="550/"></a>

* Note that "\t" stands for tab-delimitation