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: [email protected] [mailto:[email protected]] On
Behalf Of Tim Richter-Heitmann
Sent: Friday, July 11, 2014 9:16 AM
To: [email protected]
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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and provide commented, minimal, self-contained, reproducible code.
