integrating 2 lists and a data frame in R

On Jun 6, 2017, at 4:01 AM, Jim Lemon <drjimlemon at gmail.com> wrote:

Hi Bogdan,
Kinda messy, but:

N <- data.frame(N=c("n1","n2","n3","n4"))
M <- data.frame(M=c("m1","m2","m3","m4","m5"))
C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"),

I=c(100,300,400))

MN<-as.data.frame(matrix(NA,nrow=length(N[,1]),ncol=length(M[,1])))
names(MN)<-M[,1]
rownames(MN)<-N[,1]
C[,1]<-as.character(C[,1])
C[,2]<-as.character(C[,2])
for(row in 1:dim(C)[1]) MN[C[row,1],C[row,2]]<-C[row,3]

`xtabs` offers another route:

C$m <- factor(C$m, levels=M$M)
C$n <- factor(C$n, levels=N$N)

Option 1:  Zeroes in the empty positions:

(X <- xtabs(I ~ m+n , C, addNA=TRUE))

    n
m     n1  n2  n3  n4
  m1 100 300   0   0
  m2   0   0   0   0
  m3   0   0 400   0
  m4   0   0   0   0
  m5   0   0   0   0

Option 2: Sparase matrix

(X <- xtabs(I ~ m+n , C, sparse=TRUE))

5 x 4 sparse Matrix of class "dgCMatrix"
    n
m     n1  n2  n3 n4
  m1 100 300   .  .
  m2   .   .   .  .
  m3   .   . 400  .
  m4   .   .   .  .
  m5   .   .   .  .

I wasn't sure if the sparse reuslts of xtabs would make a distinction
between 0 and NA, but happily it does:

C <- data.frame(n=c("n1","n2","n3", "n3", "n4"), m=c("m1","m1","m3",

"m4", "m5"), I=c(100,300,400, NA, 0))

C

   n  m   I
1 n1 m1 100
2 n2 m1 300
3 n3 m3 400
4 n3 m4  NA
5 n4 m5   0

(X <- xtabs(I ~ m+n , C, sparse=TRUE))

4 x 4 sparse Matrix of class "dgCMatrix"
    n
m     n1  n2  n3 n4
  m1 100 300   .  .
  m3   .   . 400  .
  m4   .   .   .  .
  m5   .   .   .  0

(In the example I forgot to repeat the lines that augmented the factor
levels so m2 is not seen.

--
Davod

Jim

On Tue, Jun 6, 2017 at 3:51 PM, Bogdan Tanasa <tanasa at gmail.com> wrote:

Dear Bert,

thank you for your response. here it is the piece of R code : given 3

data

frames below ---

N <- data.frame(N=c("n1","n2","n3","n4"))

M <- data.frame(M=c("m1","m2","m3","m4","m5"))

C <- data.frame(n=c("n1","n2","n3"), m=c("m1","m1","m3"),

I=c(100,300,400))

how shall I integrate N, and M, and C in such a way that at the end we

have

a data frame with :


  - list N as the columns names
  - list M as the rows names
  - the values in the cells of N * M, corresponding to the numerical
  values in the data frame C.

more precisely, the result shall be :

    n1  n2  n3 n4
m1  100  200   -   -
m2   -   -   -   -
m3   -   -   300   -
m4   -   -   -   -
m5   -   -   -   -

thank you !


On Mon, Jun 5, 2017 at 6:57 PM, Bert Gunter <bgunter.4567 at gmail.com>

wrote:

Reproducible example, please. -- In particular, what exactly does C

look

ilike?

(You should know this by now).

-- Bert
Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, Jun 5, 2017 at 6:45 PM, Bogdan Tanasa <tanasa at gmail.com>

wrote:

Dear all,

please could you advise on the R code I could use in order to do the
following operation :

a. -- I have 2 lists of "genome coordinates" : a list is composed by
numbers that represent genome coordinates;

let's say list N :

n1

n2

n3

n4

and a list M:

m1

m2

m3

m4

m5

2 -- and a data frame C, where for some pairs of coordinates (n,m)

from

the

lists above, we have a numerical intensity;

for example :

n1; m1; 100

n1; m2; 300

The question would be : what is the most efficient R code I could use

in

order to integrate the list N, the list M, and the data frame C, in

order

to obtain a DATA FRAME,

-- list N as the columns names
-- list M as the rows names
-- the values in the cells of N * M, corresponding to the numerical

values

in the data frame C.

A little example would be :

     n1  n2  n3 n4

     m1  100  -   -   -

     m2  300  -   -   -

     m3   -   -   -   -

     m4   -   -   -   -

     m5   -   -   -   -
I wrote a script in perl, although i would like to do this in R
Many thanks ;)
-- bogdan

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David Winsemius
Alameda, CA, USA