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S Peri

2004-Jul-08 02:56 UTC

[R] read.frame

Hello group, 
  I am learning R and I am new to many concepts.I face
the following errors when I am trying to execute the
following. I have 4 text files with protein accession
numbers. I wanted to represent them in a venn diagram
and for that I using intersect and setdiff functions.

My data looks like this:

file1.txt (c):
NP_000005
NP_000020
NP_000030
NP_000053

file2.txt(e):
NP_000005
NP_000020
NP_000030
NP_000031
NP_000053
NP_000055
NP_000087

file3.txt(h):
NP_000005
NP_000020
NP_000030
NP_000053
NP_000055
NP_000057
NP_000087

file4.txt (s):
NP_000005
NP_000020
NP_000030
NP_000033
NP_000053
NP_000055
NP_000087
NP_000168


Now I did the following FIRST time:
c=read.table("file1.txt")
e=read.table("file2.txt")
s=read.table("file4.txt")
h=read.table("file3.txt")
> class(c)
[1] "data.frame"> class(s)
[1] "data.frame"> CiS=intersect(c,s)
> CiSNULL data frame with 0 rows 
##### Why am I getting NULL data error. I know there
are common elements between c and S. ##########
> CiS<-intersect(read.matrix(c,s))Error in unique(y[match(x, y, 0)]) : Argument "y" is
missing, with no default> CiS<-intersect(read.frame(c,s))Error in unique(y[match(x, y, 0)]) : Argument "y" is
missing, with no default

##### Why am I getting this error.



Second thing I did:

I loaded the data as data.frame instead read.table(). 
Again I never get intersection of C,E and S,H. 


Can any one please help me. 
thank you

SP

Alec Stephenson

2004-Jul-08 03:24 UTC

head link

[R] read.frame

The help file on the intersect function says
     Performs set union, intersection, (asymmetric!) difference,
     equality and membership on two vectors.

and so intersect(s[,1],c[,1]) is probably what you want.

Alec

Alec Stephenson                                               
Department of Statistics
Macquarie University
NSW 2109, Australia 
>>> S Peri <biocperi at yahoo.com> 07/08/04 12:56pm >>>Hello group, 
  I am learning R and I am new to many concepts.I face
the following errors when I am trying to execute the
following. I have 4 text files with protein accession
numbers. I wanted to represent them in a venn diagram
and for that I using intersect and setdiff functions.

My data looks like this:

file1.txt (c):
NP_000005
NP_000020
NP_000030
NP_000053

file2.txt(e):
NP_000005
NP_000020
NP_000030
NP_000031
NP_000053
NP_000055
NP_000087

file3.txt(h):
NP_000005
NP_000020
NP_000030
NP_000053
NP_000055
NP_000057
NP_000087

file4.txt (s):
NP_000005
NP_000020
NP_000030
NP_000033
NP_000053
NP_000055
NP_000087
NP_000168


Now I did the following FIRST time:
c=read.table("file1.txt")
e=read.table("file2.txt")
s=read.table("file4.txt")
h=read.table("file3.txt")
> class(c)
[1] "data.frame"> class(s)
[1] "data.frame"> CiS=intersect(c,s)
> CiSNULL data frame with 0 rows 
##### Why am I getting NULL data error. I know there
are common elements between c and S. ##########
> CiS<-intersect(read.matrix(c,s))Error in unique(y[match(x, y, 0)]) : Argument "y" is
missing, with no default> CiS<-intersect(read.frame(c,s))Error in unique(y[match(x, y, 0)]) : Argument "y" is
missing, with no default

##### Why am I getting this error.



Second thing I did:

I loaded the data as data.frame instead read.table(). 
Again I never get intersection of C,E and S,H. 


Can any one please help me. 
thank you

SP

______________________________________________
R-help at stat.math.ethz.ch mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help 
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

S Peri

2004-Jul-08 04:41 UTC

head link

[R] read.frame

Dear Alec, 
 Thank you for your response and it worked. Further, I
have another mathematical problem. I apologize ahead
as this question is not apt for this list. I am a
biologist working at Johns Hopkins School of Medicine.

As I listed in my previous e-mail (attached below)I
mentioned I have 4 protein sets.  I am now trying to
calculate the combinatorics of these sets.  My
ultimate aim is to draw a venn diagram and find out
the proteins that are unique to set C,S,E and H. 
 I drew a venn diagram graph and I am banging my head
to deduce the combinations.  It is easy for me to
deduce the intersections - that means the protein
entries that are present in common. However, it proved
very difficult to deduce the following: 

I could calculate the following:

NP_*** present in both C and E (C intersection E)
NP_*** present in both C and H (C intersection H)
NP_*** present in both C and S (C ^ S)
NP_*** present in both E and H (E ^ H)
NP_*** present in both E and S (E ^ S)
NP_*** present in both H and S (H ^ S)

NP_*** present in C, E and H (C^E^H)
NP_*** present in C, H and S (C^H^S)
NP_*** present in E, H and S (E^H^S)
NP_*** present in E, S and C (E^S^C)

It is very difficult for me to deduce the following:

NP_**** entries specific to E
NP_**** entries specific to H
NP_**** entries specific to S

I waster many pages but could not derive some solution
to get unique elements for sets, s,e,h,and C.

Can any one help me by suggesting some way to get
these.

Thank you and I apologise again for posting the wrong
question. 

SP

--- S Peri <biocperi at yahoo.com> wrote:> Hello group, 
>   I am learning R and I am new to many concepts.I
> face
> the following errors when I am trying to execute the
> following. I have 4 text files with protein
> accession
> numbers. I wanted to represent them in a venn
> diagram
> and for that I using intersect and setdiff
> functions.
> 
> My data looks like this:
> 
> file1.txt (c):
> NP_000005
> NP_000020
> NP_000030
> NP_000053
> 
> file2.txt(e):
> NP_000005
> NP_000020
> NP_000030
> NP_000031
> NP_000053
> NP_000055
> NP_000087
> 
> file3.txt(h):
> NP_000005
> NP_000020
> NP_000030
> NP_000053
> NP_000055
> NP_000057
> NP_000087
> 
> file4.txt (s):
> NP_000005
> NP_000020
> NP_000030
> NP_000033
> NP_000053
> NP_000055
> NP_000087
> NP_000168
> 
> 
> Now I did the following FIRST time:
> c=read.table("file1.txt")
> e=read.table("file2.txt")
> s=read.table("file4.txt")
> h=read.table("file3.txt")
> 
> > class(c)
> [1] "data.frame"
> > class(s)
> [1] "data.frame"
> > CiS=intersect(c,s)
> > CiS
> NULL data frame with 0 rows 
> ##### Why am I getting NULL data error. I know there
> are common elements between c and S. ##########
> 
> > CiS<-intersect(read.matrix(c,s))
> Error in unique(y[match(x, y, 0)]) : Argument "y" is
> missing, with no default
> > CiS<-intersect(read.frame(c,s))
> Error in unique(y[match(x, y, 0)]) : Argument "y" is
> missing, with no default
> 
> ##### Why am I getting this error.
> 
> 
> 
> Second thing I did:
> 
> I loaded the data as data.frame instead
> read.table(). 
> Again I never get intersection of C,E and S,H. 
> 
> 
> Can any one please help me. 
> thank you
> 
> SP
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
>
https://www.stat.math.ethz.ch/mailman/listinfo/r-help> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>

DJNordlund@aol.com

2004-Jul-08 05:35 UTC

head link

[R] read.frame

In a message dated 7/7/2004 9:42:03 PM Pacific Daylight Time,  
biocperi@yahoo.com writes:

Dear  Alec, 
Thank you for your response and it worked. Further, I
have  another mathematical problem. I apologize ahead
as this question is not apt  for this list. I am a
biologist working at Johns Hopkins School of  Medicine.

As I listed in my previous e-mail (attached  below)I
mentioned I have 4 protein sets.  I am now trying  to
calculate the combinatorics of these sets.  My
ultimate aim is  to draw a venn diagram and find out
the proteins that are unique to set  C,S,E and H. 
I drew a venn diagram graph and I am banging my head
to  deduce the combinations.  It is easy for me to
deduce the  intersections - that means the protein
entries that are present in common.  However, it proved
very difficult to deduce the following: 

I could  calculate the following:

NP_*** present in both C and E (C intersection  E)
NP_*** present in both C and H (C intersection H)
NP_*** present in  both C and S (C ^ S)
NP_*** present in both E and H (E ^ H)
NP_***  present in both E and S (E ^ S)
NP_*** present in both H and S (H ^  S)

NP_*** present in C, E and H (C^E^H)
NP_*** present in C, H and S  (C^H^S)
NP_*** present in E, H and S (E^H^S)
NP_*** present in E, S and  C (E^S^C)


It is very difficult for me to deduce the  following:

NP_**** entries specific to E
NP_**** entries specific to  H
NP_**** entries specific to S





I am not sure about your notation, but in R terms, if you want the items  
specific to E, H, or S, how about something like:
 
specific to E  --   setdiff(e, union(c,union(h,s)))
 
specific to H  --   setdiff(h,  union(c,union(e,s)))
 
specific to S  --   setdiff(s,  union(c,union(e,h)))
 
Dan Nordlund



	[[alternative HTML version deleted]]

Alec Stephenson

2004-Jul-08 07:25 UTC

head link

[R] read.frame

For E:
e <- e[,1] ; uni <- union(c[,1],union(s[,1],h[,1]))
Then e[!match(e, uni, 0)] should get you there. 

Alec

Alec Stephenson                                               
Department of Statistics
Macquarie University
NSW 2109, Australia 
>>> S Peri <biocperi at yahoo.com> 07/08/04 02:41pm >>>Dear Alec, 
 Thank you for your response and it worked. Further, I
have another mathematical problem. I apologize ahead
as this question is not apt for this list. I am a
biologist working at Johns Hopkins School of Medicine.

As I listed in my previous e-mail (attached below)I
mentioned I have 4 protein sets.  I am now trying to
calculate the combinatorics of these sets.  My
ultimate aim is to draw a venn diagram and find out
the proteins that are unique to set C,S,E and H. 
 I drew a venn diagram graph and I am banging my head
to deduce the combinations.  It is easy for me to
deduce the intersections - that means the protein
entries that are present in common. However, it proved
very difficult to deduce the following: 

I could calculate the following:

NP_*** present in both C and E (C intersection E)
NP_*** present in both C and H (C intersection H)
NP_*** present in both C and S (C ^ S)
NP_*** present in both E and H (E ^ H)
NP_*** present in both E and S (E ^ S)
NP_*** present in both H and S (H ^ S)

NP_*** present in C, E and H (C^E^H)
NP_*** present in C, H and S (C^H^S)
NP_*** present in E, H and S (E^H^S)
NP_*** present in E, S and C (E^S^C)


It is very difficult for me to deduce the following:

NP_**** entries specific to E
NP_**** entries specific to H
NP_**** entries specific to S


I waster many pages but could not derive some solution
to get unique elements for sets, s,e,h,and C.

Can any one help me by suggesting some way to get
these.

Thank you and I apologise again for posting the wrong
question. 

SP


--- S Peri <biocperi at yahoo.com> wrote:> Hello group, 
>   I am learning R and I am new to many concepts.I
> face
> the following errors when I am trying to execute the
> following. I have 4 text files with protein
> accession
> numbers. I wanted to represent them in a venn
> diagram
> and for that I using intersect and setdiff
> functions.
> 
> My data looks like this:
> 
> file1.txt (c):
> NP_000005
> NP_000020
> NP_000030
> NP_000053
> 
> file2.txt(e):
> NP_000005
> NP_000020
> NP_000030
> NP_000031
> NP_000053
> NP_000055
> NP_000087
> 
> file3.txt(h):
> NP_000005
> NP_000020
> NP_000030
> NP_000053
> NP_000055
> NP_000057
> NP_000087
> 
> file4.txt (s):
> NP_000005
> NP_000020
> NP_000030
> NP_000033
> NP_000053
> NP_000055
> NP_000087
> NP_000168
> 
> 
> Now I did the following FIRST time:
> c=read.table("file1.txt")
> e=read.table("file2.txt")
> s=read.table("file4.txt")
> h=read.table("file3.txt")
> 
> > class(c)
> [1] "data.frame"
> > class(s)
> [1] "data.frame"
> > CiS=intersect(c,s)
> > CiS
> NULL data frame with 0 rows 
> ##### Why am I getting NULL data error. I know there
> are common elements between c and S. ##########
> 
> > CiS<-intersect(read.matrix(c,s))
> Error in unique(y[match(x, y, 0)]) : Argument "y" is
> missing, with no default
> > CiS<-intersect(read.frame(c,s))
> Error in unique(y[match(x, y, 0)]) : Argument "y" is
> missing, with no default
> 
> ##### Why am I getting this error.
> 
> 
> 
> Second thing I did:
> 
> I loaded the data as data.frame instead
> read.table(). 
> Again I never get intersection of C,E and S,H. 
> 
> 
> Can any one please help me. 
> thank you
> 
> SP
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
>
https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html 
>
______________________________________________
R-help at stat.math.ethz.ch mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help 
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

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