Converting a data frame with values into a matrix/
The way that you have set up the data.frame is rather
unusual. It makes NES a factor which I suspect you
don't want. Do str(xx) to see what I mean
Here is a way that I think does what you want but with
the data.frame constructed in a different manner.
Again do str(aa) to see the difference
=====================================================
aa <- data.frame(Name=c( "Mike" ,"Carl", "Gene",
"James","Dough"),
Class=c( "A", "A", "C", "A", "B"),
NES=c( 0.01, 0.2, 0.3, -0.3, 0) )
aa
library(reshape)
mm <- melt(aa, id=c("Name", "Class"))
mm1 <- cast(mm, Class~Name)
aba <- mm1[,2:6]
aba[is.na(aba)] <- 1
final <- data.frame(mm1$Class, aba)
names(final) <- names(mm1)
final
===================================================
--- Srinivas Iyyer <srini_iyyer_bio at yahoo.com> wrote:
Dear Group,
I have a data frame like the following:
x <- c("Mike","A",0.01)
x1 <- c("Carl","A",0.2)
x2 <- c("Gene","C",0.3)
x3 <- c("James","A",-0.3)
x4 <- c("Dough","B",0)
xx <- rbind(x,x1,x2,x3,x4)
colnames(xx)<-c("Name","Class","NES")
xx <-as.data.frame(xx)
xx
Name Class NES x Mike A 0.01 x1 Carl A 0.2 x2 Gene C 0.3 x3 James A -0.3 x4 Dough B 0 Now I want to create a matrix with unique xx$Name on columns and unique xx$Class as rows. I want to fill my choice of values (in this case 1) if data point not available. xy <-
matrix(1,length(unique(xx$Class)),length(unique(xx[,1])))
colnames(xy)<-unique(xx[,1]) rownames(xy)<-unique(xx$Class)
xy
Mike Carl Gene James Dough A 1 1 1 1 1 C 1 1 1 1 1 B 1 1 1 1 1 I would love to have : Mike Carl Gene James Dough A 0.01 0.2 1 -0.3 1 C 1 1 1 0.3 1 B 1 1 1 1 0 If I am not wrong this is called contigency or frequeny table. I tried xtabs on this.
z <- xtabs(NES ~ Name+Class,data=xx)
Error in Summary.factor(4L, na.rm = FALSE) : sum not meaningful for factors I tried on other data frames, it worked. BUT the problem is it gives me 0.0000 even a value is not available for that row and column. So if I have data -0.00 it is considered 0. I tried. drop.unused.levels = T, I did not get what I want. I want all row.col values not available to be 1. Is there any other trick where I map by row and column names instead of using advanced xtabs. thanks Srini
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