[R] Problems with read.table and data structure

[Marc Schwartz]

On Jul 11, 2014, at 9:15 AM, Tim Richter-Heitmann <trichter at uni-bremen.de> wrote:

> Hi there!
> 
> I have huge datafile of 600 columns 360 samples:
> 
> data <- read.table("small.txt", header = TRUE, sep = "\t", dec = ".", 
> row.names=1)
> 
> The txt.file (compiled with excel) is showing me only numbers, however R 
> gives me the structure of ANY column as "factor".
> 
> When i try "stringsAsFactors=FALSE" in the read command, the structure 
> of the dataset becomes "character."
> 
> When i try as.numeric(data), i get
> 
> Error: (list) object cannot be coerced to type 'double'
> 
> 
> even, if i try to subset columns with [].
> 
> 
> When i try as.numeric on single columns with $, i am successful, but the numbers dont make any sense at all, as the factors are not converted by their levels:
> 
> 
> Factor w/ 358 levels "0,123111694",..: 11 14 50 12 38 44 13 76 31 30
> 
> 
> becomes
> 
> 
> num  11 14 50 12 38 44 13 76 31 30
> 
> 
> whereas i would need the levels, though!
> 
> 
> I suspect excel to mess up the "save as tab-delimited text", but the text file seems fine with me on surface (i dont know how the numbers are stored  internally). I just see correct numbers, also the View command
> yields the correct content.
> 
> 
> 
> Anyone knows help? Its pretty annoying.
> 
> 
> 
> Thank you!


Hi,

See:

  http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-do-I-convert-factors-to-numeric_003f

Regards,

Marc Schwartz