R help - Jul 2009 - How to provide list as an argument for the data.frame()

Hi R -users,

i've a table as describe below. I'm reading the numeric value presented
in this table to populate a list.

#table
#===========#X    A    B    C
#x1    2    3    4
#x2    5    7    10
#x4    2    3    5
#===========
rawData <- read.table("raw_data.txt",header=T, sep="\t")
myList=list()
counter=0
for (i in c(1:length(rawData$X)))
{
    print (i)
    myList[counter <- counter +1]=as.numeric(rawData$A[i]);
    myList[counter <- counter +1]=as.numeric(rawData$B[i]);
    myList[counter <- counter +1]=as.numeric(rawData$C[i]);   
}
print(myList)

comp <- factor(rep(c("A","B","C"),c(3,3,3)))
cell <- factor(rep(c("x1","x2","x3"),3))

t <- data.frame(comp,cell)
print(t)

i'm looking for the output show below
#  comp cell value
#1    A   x1   2
#2    A   x2   5
#3    A   x3   2
#4    B   x1   3
#5    B   x2   7
#6    B   x3   3
#7    C   x1   4
#8    C   x2   10
#9    C   x3   5

Help needed as how i should provide list as a third argument to data.frame().

Thanks in advance.


Gaurav Kumar
www.gauravkumar.org

PhD Student, Chemistry and Biomolecular Sciences, Macquarie , Sydney, Australia.
MS (Computational Biology), NCBS-TIFR, Bangalore, India.


	[[alternative HTML version deleted]]

On Jul 14, 2009, at 8:14 AM, Gaurav Kumar wrote:
> Hi R -users,
>
> i've a table as describe below. I'm reading the numeric value  
> presented in this table to populate a list.
>
> #table
> #===========> #X    A    B    C
> #x1    2    3    4
> #x2    5    7    10
> #x4    2    3    5
> #===========>
> rawData <- read.table("raw_data.txt",header=T,
sep="\t")
> myList=list()
> counter=0
> for (i in c(1:length(rawData$X)))
> {
>     print (i)
>     myList[counter <- counter +1]=as.numeric(rawData$A[i]);
>     myList[counter <- counter +1]=as.numeric(rawData$B[i]);
>     myList[counter <- counter +1]=as.numeric(rawData$C[i]);
> }
> print(myList)
>
> comp <-
factor(rep(c("A","B","C"),c(3,3,3)))
> cell <- factor(rep(c("x1","x2","x3"),3))
>
> t <- data.frame(comp,cell)
> print(t)
>
> i'm looking for the output show below
> #  comp cell value
> #1    A   x1   2
> #2    A   x2   5
> #3    A   x3   2
> #4    B   x1   3
> #5    B   x2   7
> #6    B   x3   3
> #7    C   x1   4
> #8    C   x2   10
> #9    C   x3   5
>
> Help needed as how i should provide list as a third argument to  
> data.frame().

To answer your narrow question:

?unlist


But wouldn't it have been a lot easier to to this, and skip all that C  
style looping?

cbind(cell=factor(rep(c("x1","x2","x3"),3)),
stack(rawData) )
###
   cell values ind
1   x1      2   A
2   x2      5   A
3   x3      2   A
4   x1      3   B
5   x2      7   B
6   x3      3   B
7   x1      4   C
8   x2     10   C
9   x3      5   C
>
> Thanks in advance.
>
>
> Gaurav Kumar
> www.gauravkumar.org
>
> PhD Student, Chemistry and Biomolecular Sciences, Macquarie ,  
> Sydney, Australia.
> MS (Computational Biology), NCBS-TIFR, Bangalore, India.
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org 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.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT

On Jul 14, 2009, at 7:14 AM, Gaurav Kumar wrote:
> Hi R -users,
>
> i've a table as describe below. I'm reading the numeric value  
> presented in this table to populate a list.
>
> #table
> #===========> #X    A    B    C
> #x1    2    3    4
> #x2    5    7    10
> #x4    2    3    5
> #===========>
> rawData <- read.table("raw_data.txt",header=T,
sep="\t")
> myList=list()
> counter=0
> for (i in c(1:length(rawData$X)))
> {
>     print (i)
>     myList[counter <- counter +1]=as.numeric(rawData$A[i]);
>     myList[counter <- counter +1]=as.numeric(rawData$B[i]);
>     myList[counter <- counter +1]=as.numeric(rawData$C[i]);
> }
> print(myList)
>
> comp <-
factor(rep(c("A","B","C"),c(3,3,3)))
> cell <- factor(rep(c("x1","x2","x3"),3))
>
> t <- data.frame(comp,cell)
> print(t)
>
> i'm looking for the output show below
> #  comp cell value
> #1    A   x1   2
> #2    A   x2   5
> #3    A   x3   2
> #4    B   x1   3
> #5    B   x2   7
> #6    B   x3   3
> #7    C   x1   4
> #8    C   x2   10
> #9    C   x3   5
>
> Help needed as how i should provide list as a third argument to  
> data.frame().
>
> Thanks in advance.
Read your data in as follows:

# Set the rownames to the values in 'X' and coerce to a matrix
rawData <- as.matrix(read.table("raw_data.txt", header = TRUE,
                                 sep = "\t", row.names =
"X"))


# Note that you have 'x3' in your results, but 'x4' was in the
# initial data table, so I kept 'x4'
 > rawData
    A B  C
x1 2 3  4
x2 5 7 10
x4 2 3  5


# Set the row and column names
names(dimnames(rawData)) <- list("cell", "comp")

 > rawData
     comp
cell A B  C
   x1 2 3  4
   x2 5 7 10
   x4 2 3  5


# See ?as.data.frame.table
 > as.data.frame.table(rawData, responseName = "value")
   cell comp value
1   x1    A     2
2   x2    A     5
3   x4    A     2
4   x1    B     3
5   x2    B     7
6   x4    B     3
7   x1    C     4
8   x2    C    10
9   x4    C     5


HTH,

Marc Schwartz