Here is one way of doing it using the reshape package:
> # test data from email
> x <- "$$ Experiment Number:
+ $$ Associated Data:
+
+ FUNCTION 1
+
+ Scan 1
+ Retention Time 0.017
+
+ 399.8112 184
+ 399.8742 0
+ 399.9372 152
+ ....
+
+ Scan 2
+ Retention Time 0.021
+
+ 399.8112 181
+ 399.8742 1
+ 399.9372 153
+ .....
+ "
> # read in the vector
> x.in <- readLines(textConnection(x))
> result <- list() # output list
> i.result <- 1
> # process each line
> for (i in x.in){
+ # if Retention, pick off the time
+ if (regexpr("^Retention", i) > 0){
+ time <- gsub("^Ret.*?([0-9.]+)", "\\1", i, perl=TRUE)
+ } else if (regexpr("^\\d+", i, perl=TRUE) > 0){
+ # if data, parse it and store in result
+ idVal <- strsplit(i, "\\s+")
+ result[[i.result]] <- c(time, idVal[[1]])
+ i.result <- i.result + 1
+ }
+ }
> # create data frame
> df <- as.data.frame(do.call(rbind, result))
> colnames(df) <- c('time', 'id', 'value')
> require(reshape) # use reshape package
Loading required package: reshape
[1] TRUE
> y <- melt(df)
> # convert to long
> cast(y, time ~ id)
time X399.8112 X399.8742 X399.9372
1 0.017 184 0 152
2 0.021 181 1 153
>
>
Jim Holtman
"What is the problem you are trying to solve?"
----- Original Message ----
From: Gabor Grothendieck <[EMAIL PROTECTED]>
To: Bart Joosen <[EMAIL PROTECTED]>
Cc: r-help@stat.math.ethz.ch
Sent: Thursday, March 1, 2007 12:35:43 PM
Subject: Re: [R] How to read in this data format?
Read in the data using readLines, extract out
all desired lines (namely those containing only
numbers, dots and spaces or those with the
word Time) and remove Retention from all
lines so that all remaining lines have two
fields. Now that we have desired lines
and all lines have two fields read them in
using read.table.
Finally, split them into groups and restructure
them using "by" and in the last line we
convert the "by" output to a data frame.
At the end we display an alternate function f
for use with by should we wish to generate long
rather than wide output (using the terminology
of the reshape command).
Lines <- "$$ Experiment Number:
$$ Associated Data:
FUNCTION 1
Scan 1
Retention Time 0.017
399.8112 184
399.8742 0
399.9372 152
....
Scan 2
Retention Time 0.021
399.8112 181
399.8742 1
399.9372 153
"
# replace next line with: Lines. <- readLines("myfile.dat")
Lines. <- readLines(textConnection(Lines))
Lines. <- grep("^[1-9][0-9. ]*$|Time", Lines., value = TRUE)
Lines. <- gsub("Retention", "", Lines.)
DF <- read.table(textConnection(Lines.), as.is = TRUE)
closeAllConnections()
f <- function(x) c(id = x[1,2], structure(x[-1,2], .Names = x[-1,1]))
out.by <- by(DF, cumsum(DF[,1] == "Time"), f)
as.data.frame(do.call("rbind", out.by))
We could alternately consider producing long
format by replacing the function f with:
f <- function(x) data.frame(x[-1,], id = x[1,2])
On 3/1/07, Bart Joosen <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I recieved an ascii file, containing following information:
>
> $$ Experiment Number:
> $$ Associated Data:
>
> FUNCTION 1
>
> Scan 1
> Retention Time 0.017
>
> 399.8112 184
> 399.8742 0
> 399.9372 152
> ....
>
> Scan 2
> Retention Time 0.021
>
> 399.8112 181
> 399.8742 1
> 399.9372 153
> .....
>
>
> I would like to import this data in R into a dataframe, where there is a
> column time, the first numbers as column names, and the second numbers as
> data in the dataframe:
>
> Time 399.8112 399.8742 399.9372
> 0.017 184 0 152
> 0.021 181 1 153
>
> I did take a look at the read.table, read.delim, scan, ... But I 've no idea
> about how to solve this problem.
>
> Anyone?
>
>
> Thanks
>
> Bart
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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