[R] Reading a file with read.csv: two character rows not interpreted as I hope

[jim holtman]

Here is one way.  You will probably use 'file' instead of textConnection

> x.in <- textConnection('wavelength SampleA SampleB SampleC SampleD
+  color "green" "black" "black" "green"
+  class "Class 1" "Class 2" "Class 2" "Class 1"
+  403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
+  409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
+  415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
+  420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
+  426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
+  432 1.42E-01 1.50E-01 1.62E-01 1.48E-01')
>
> c.names <- scan(x.in, what='', nlines=1)  # read column names
Read 5 items
> c.options <- read.table(x.in, as.is=TRUE, nrows=2) # get lines 2-3
> c.data <- read.table(x.in)  # rest of the data
> colnames(c.data) <- c.names
> close(x.in)
> c.options  # here are lines 2-3
     V1      V2      V3      V4      V5
1 color   green   black   black   green
2 class Class 1 Class 2 Class 2 Class 1
> c.data  # your data
  wavelength SampleA SampleB SampleC SampleD
1        403   0.194   0.214   0.211   0.183
2        409   0.192   0.189   0.200   0.182
3        415   0.170   0.199   0.194   0.186
4        420   0.159   0.191   0.216   0.174
5        426   0.150   0.166   0.172   0.158
6        432   0.142   0.150   0.162   0.148


On 10/30/07, Bryan Hanson <hanson at depauw.edu> wrote:
> Hi Folks... Œbeen playing with this for a while, with no luck, so I¹m hoping
> someone knows it off the top of their head...  Difficult to find this nuance
> in the archives, as so many msgs deal with read.csv!
>
> I¹m trying to read a data file with the following structure (a little piece
> of the actual data, they are actually csv just didn¹t paste with the
> commas):
>
>  wavelength SampleA SampleB SampleC SampleD
>  color "green" "black" "black" "green"
>  class "Class 1" "Class 2" "Class 2" "Class 1"
>  403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
>  409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
>  415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
>  420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
>  426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
>  432 1.42E-01 1.50E-01 1.62E-01 1.48E-01
>
> Columns after the first one are sample names.  2nd row is the list of colors
> to use in later plotting.  3rd row is the class for later manova.  The rest
> of it is x data in the first column with y1, y2...following for plotting.
>
> I can read the file w/o the color or class rows with read.csv just fine,
> makes a nice data frame with proper data types.  The problem comes when
> parsing the 2nd and 3rd rows.  Here¹s the code:
>
> data = read.csv("filename", header=TRUE) # read in data
> color = data[1,]; color = data[-1] # capture color info & throw out 1st
> value
> class = data[2,]; class = class[-1] # capture category info & throw out 1st
> value
>
> cleaned.data = data[-1,] # remove color & category info for matrix
> operations
> cleaned.data = data[-1,]
> freq = data[,1] # capture frequency info
>
> What happens is that freq is parsed as factors, and the color and class are
> parsed as a data frames of factors.
> I need color and class to be characters which I can pass to functions in the
> typical way one uses colors and levels.
> I need the freq & the cleaned.data info as numeric for plotting.
>
> I don¹t feel I¹m far off from things working, but that¹s where you all come
> in!  Seems like an argument of as.something is needed, but the ones I¹ve
> tried don¹t work.  Would it help to put color and class above the x,y data
> in the file, then clean it off?
>
> Btw, I¹m on a Mac using R 2.6.0.
>
> Thanks in advance, Bryan
> *************
> Bryan Hanson
> Professor of Chemistry & Biochemistry
>
>
>
>
>        [[alternative HTML version deleted]]
>
>
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>


-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?