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Min-Han Tan

2010-May-06 19:27 UTC

[R] Apologies : question on transforming a table

Dear R-help list,

Apologies. I  am trying to convert one table to another. It feels that it
should be a very straightforward answer with a single (or two) commands with
the right extensions, but I really can't figure this out right now. I have
several hundred pheno factors actually, so manually doing this line by line
is not an option.

My original table is approximately like this :

   ID         pheno
1   A Breast Cancer
2   A  Appendicitis
3   A  Microcephaly
4   B        Polyps
5   B        Autism
6   C        Autism
7   D Breast Cancer
8   D        Polyps
9   D  Appendicitis
10  E Breast Cancer


What I want is this :
    ID Breast Cancer Appendicitis Microcephaly Polyps Autism  A 1 1 1   B  1
1  C   1  D 1  1  E 1

The data is here
data <-
data.frame(ID=c(rep("A",3),rep("B",2),rep("C",1),rep("D",3),rep("E",1)),
pheno=c("Breast
Cancer","Appendicitis","Microcephaly","Polyps","Autism","Autism","Breast
Cancer","Polyps","Appendicitis","Breast
Cancer"))

Thank you very much! Many apologies.

Min-Han

	[[alternative HTML version deleted]]

Joachim de Lezardiere

2010-May-06 19:38 UTC

head link

[R] Apologies : question on transforming a table

Can you explain more about the output you want  ? 

Thank you

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On
Behalf Of Min-Han Tan
Sent: Thursday, May 06, 2010 2:28 PM
To: r-help at stat.math.ethz.ch
Subject: [R] Apologies : question on transforming a table

Dear R-help list,

Apologies. I  am trying to convert one table to another. It feels that it
should be a very straightforward answer with a single (or two) commands with
the right extensions, but I really can't figure this out right now. I have
several hundred pheno factors actually, so manually doing this line by line
is not an option.

My original table is approximately like this :

   ID         pheno
1   A Breast Cancer
2   A  Appendicitis
3   A  Microcephaly
4   B        Polyps
5   B        Autism
6   C        Autism
7   D Breast Cancer
8   D        Polyps
9   D  Appendicitis
10  E Breast Cancer

What I want is this :
    ID Breast Cancer Appendicitis Microcephaly Polyps Autism  A 1 1 1   B  1
1  C   1  D 1  1  E 1

The data is here
data <-
data.frame(ID=c(rep("A",3),rep("B",2),rep("C",1),rep("D",3),rep("E",1)),
pheno=c("Breast
Cancer","Appendicitis","Microcephaly","Polyps","Autism","Autism","Breast
Cancer","Polyps","Appendicitis","Breast
Cancer"))

Thank you very much! Many apologies.

Min-Han

	[[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

2010-May-06 19:47 UTC

head link

[R] Apologies : question on transforming a table

On May 6, 2010, at 3:27 PM, Min-Han Tan wrote:
> Dear R-help list,
>
> Apologies. I  am trying to convert one table to another. It feels  
> that it
> should be a very straightforward answer with a single (or two)  
> commands with
> the right extensions, but I really can't figure this out right now.  
> I have
> several hundred pheno factors actually, so manually doing this line  
> by line
> is not an option.
>
> My original table is approximately like this :
>
>   ID         pheno
> 1   A Breast Cancer
> 2   A  Appendicitis
> 3   A  Microcephaly
> 4   B        Polyps
> 5   B        Autism
> 6   C        Autism
> 7   D Breast Cancer
> 8   D        Polyps
> 9   D  Appendicitis
> 10  E Breast Cancer
>
>
> What I want is this :
>    ID Breast Cancer Appendicitis Microcephaly Polyps Autism  A 1 1  
> 1   B  1
> 1  C   1  D 1  1  E 1
>
On the off-chance, as it were, that you really want what comes across  
after html posting...

c("ID", data$pheno, unlist(sapply(1:length(tid), function(x)  
c(names(tid[x]), rep(1, tid[[x]])))) )

  [1] "ID"             "Breast\nCancer"
"Appendicitis"   "Microcephaly"
  [5] "Polyps"         "Autism"         "Autism"  
"Breast
\nCancer"
  [9] "Polyps"         "Appendicitis"   "Breast
Cancer"  "A"
[13] "1"              "1"              "1"        
"B"
[17] "1"              "1"              "C"        
"1"
[21] "D"              "1"              "1"        
"1"
[25] "E"              "1"


 >> The data is here
> data <-
>
data.frame(ID=c(rep("A",3),rep("B",2),rep("C",1),rep("D",3),rep("E",
> 1)),
> pheno=c("Breast
> Cancer 
>
","Appendicitis","Microcephaly","Polyps","Autism","Autism","Breast
> Cancer","Polyps","Appendicitis","Breast
Cancer"))
>
> Thank you very much! Many apologies.
>
> Min-Han
>
> 	[[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
West Hartford, CT

Thomas Stewart

2010-May-06 20:03 UTC

head link

[R] Apologies : question on transforming a table

This is definitely a hack, but it gets the job done.

X<-model.matrix(~0+pheno,data=data)
data2<-apply(X,2,function(X){tapply(X,data$ID,sum)})
data2

  phenoAppendicitis phenoAutism phenoBreast Cancer phenoMicrocephaly
phenoPolyps
A                 1           0                  1                 1
  0
B                 0           1                  0                 0
  1
C                 0           1                  0                 0
  0
D                 1           0                  1                 0
  1
E                 0           0                  1                 0
  0

-tgs
On Thu, May 6, 2010 at 3:27 PM, Min-Han Tan
<minhan.science@gmail.com>wrote:
> Dear R-help list,
>
> Apologies. I  am trying to convert one table to another. It feels that it
> should be a very straightforward answer with a single (or two) commands
> with
> the right extensions, but I really can't figure this out right now. I
have
> several hundred pheno factors actually, so manually doing this line by line
> is not an option.
>
> My original table is approximately like this :
>
>   ID         pheno
> 1   A Breast Cancer
> 2   A  Appendicitis
> 3   A  Microcephaly
> 4   B        Polyps
> 5   B        Autism
> 6   C        Autism
> 7   D Breast Cancer
> 8   D        Polyps
> 9   D  Appendicitis
> 10  E Breast Cancer
>
>
> What I want is this :
>    ID Breast Cancer Appendicitis Microcephaly Polyps Autism  A 1 1 1   B  1
> 1  C   1  D 1  1  E 1
>
> The data is here
> data <-
>
data.frame(ID=c(rep("A",3),rep("B",2),rep("C",1),rep("D",3),rep("E",1)),
> pheno=c("Breast
>
Cancer","Appendicitis","Microcephaly","Polyps","Autism","Autism","Breast
> Cancer","Polyps","Appendicitis","Breast
Cancer"))
>
> Thank you very much! Many apologies.
>
> Min-Han
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@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.
>
	[[alternative HTML version deleted]]

Min-Han Tan

2010-May-06 20:18 UTC

head link

[R] Apologies : question on transforming a table

Dear Bill - Thank you very much! This works perfectly!

Apologies to all those who could not visualize the formatting of the
request, I should default to plain text mail.

Thank you all once again, once again, I am very grateful to the R-help forum
for being just wonderful!

Min-Han



On Thu, May 6, 2010 at 3:38 PM, William Dunlap <wdunlap@tibco.com> wrote:
>
>
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
>
> > -----Original Message-----
> > From: r-help-bounces@r-project.org
> > [mailto:r-help-bounces@r-project.org] On Behalf Of Min-Han Tan
> > Sent: Thursday, May 06, 2010 12:28 PM
> > To: r-help@stat.math.ethz.ch
> > Subject: [R] Apologies : question on transforming a table
> >
> > Dear R-help list,
> >
> > Apologies. I  am trying to convert one table to another. It
> > feels that it
> > should be a very straightforward answer with a single (or
> > two) commands with
> > the right extensions, but I really can't figure this out
> > right now. I have
> > several hundred pheno factors actually, so manually doing
> > this line by line
> > is not an option.
> >
> > My original table is approximately like this :
> >
> >    ID         pheno
> > 1   A Breast Cancer
> > 2   A  Appendicitis
> > 3   A  Microcephaly
> > 4   B        Polyps
> > 5   B        Autism
> > 6   C        Autism
> > 7   D Breast Cancer
> > 8   D        Polyps
> > 9   D  Appendicitis
> > 10  E Breast Cancer
> >
> >
> > What I want is this :
> >     ID Breast Cancer Appendicitis Microcephaly Polyps Autism
> > A 1 1 1   B  1
> > 1  C   1  D 1  1  E 1
>
> My mailer messed up your display, but does
> table() work for you?  E.g.,
> > with(data, table(ID, pheno))
>   pheno
> ID  Appendicitis Autism Breast Cancer Microcephaly Polyps
>  A            1      0             1            1      0
>  B            0      1             0            0      1
>  C            0      1             0            0      0
>  D            1      0             1            0      1
>  E            0      0             1            0      0
>
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
>
> >
> > The data is here
> > data <-
> >
data.frame(ID=c(rep("A",3),rep("B",2),rep("C",1),rep("D",3),re
> > p("E",1)),
> > pheno=c("Breast
> >
Cancer","Appendicitis","Microcephaly","Polyps","Autism","Autis
> > m","Breast
> > Cancer","Polyps","Appendicitis","Breast
Cancer"))
> >
> > Thank you very much! Many apologies.
> >
> > Min-Han
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@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.
> >
>
	[[alternative HTML version deleted]]

Henrique Dallazuanna

2010-May-07 02:07 UTC

head link

[R] Apologies : question on transforming a table

Try dhis:

xtabs(~ ID + pheno, data = data)

On Thu, May 6, 2010 at 4:27 PM, Min-Han Tan
<minhan.science@gmail.com>wrote:
> Dear R-help list,
>
> Apologies. I  am trying to convert one table to another. It feels that it
> should be a very straightforward answer with a single (or two) commands
> with
> the right extensions, but I really can't figure this out right now. I
have
> several hundred pheno factors actually, so manually doing this line by line
> is not an option.
>
> My original table is approximately like this :
>
>   ID         pheno
> 1   A Breast Cancer
> 2   A  Appendicitis
> 3   A  Microcephaly
> 4   B        Polyps
> 5   B        Autism
> 6   C        Autism
> 7   D Breast Cancer
> 8   D        Polyps
> 9   D  Appendicitis
> 10  E Breast Cancer
>
>
> What I want is this :
>    ID Breast Cancer Appendicitis Microcephaly Polyps Autism  A 1 1 1   B  1
> 1  C   1  D 1  1  E 1
>
> The data is here
> data <-
>
data.frame(ID=c(rep("A",3),rep("B",2),rep("C",1),rep("D",3),rep("E",1)),
> pheno=c("Breast
>
Cancer","Appendicitis","Microcephaly","Polyps","Autism","Autism","Breast
> Cancer","Polyps","Appendicitis","Breast
Cancer"))
>
> Thank you very much! Many apologies.
>
> Min-Han
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@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.
>


-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O

	[[alternative HTML version deleted]]

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