[R] Problems with read.table and data structure

[David L Carlson]

It is hard to diagnose without looking at the file. For example

readLines("small.txt", n=5)

would print out the first five lines that might show problems with wrapping the lines. What does dim(data) give you? Are you getting all 360 samples and 600 columns? You could also try using the colClasses=
argument in read.table(), eg. colClasses=rep("numeric", 600). You could also have Excel save in csv format and use read.csv().

David C

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Tim Richter-Heitmann
Sent: Friday, July 11, 2014 9:16 AM
To: R-help at r-project.org
Subject: [R] Problems with read.table and data structure

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!

-- 
Tim Richter-Heitmann


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