Re: [R] a workaround for indexing a function?

2014-06-18 Thread Adam Kustka 
I noticed a missing line in the code associated with my question.  I've
re-supplied the question now with that line.

Sorry for the trouble,
Adam

 



I have a dataset of peptide 15N/14N ratios from four experiments (where
cells are grown under different conditions and were fed either 15N or 14N
nitrate aka plant food if you are interested) and I want to normalize each
of these ratios to the median 15N/14N value from all 6000 peptides from
each experiment.  Then, since these ratios (from 2 or more peptides) are
used to calculate the protein 15N/14N abundance, I want to take the median
value of all peptides belonging to one protein to calculate the overall
protein 15N/14N abundance within that experiment.



I’ve managed to break the data set into small pieces (by protein and by
experiment), which will lead to about 500 observations.



A dummy – small – dataset could look like this (below), where V1 lists the
peptides that make up a protein, V2 is the protein ID, V3 is the metric of
interest (the 15N/14N ratio of each peptide), and V4 indicates which
experiment was run.



The stumbling block here is that I cannot index the median function.



Here is what I have done so far.



y-read.table(“nameoffile.txt”)



h-split(y,y$V4)



for(n in names(h))

write.table(h[[n]], 
file=paste(y[[n]][,”V4”][4],”_”,n,”.TXT”,sep=””))



Then I (not elegantly but OK with brute force method for four files) went
into each file and calculated the median





vls1-read.table(“VLS5584_VLS5584.TXT”)  # for example, but did this four
times for each file



newcol=vls1[,3]/median(vls1[,3]) #make a new column of 15N/14N data now
normalized to median value… here this is shown for one of four experiments.




normvls1=cbind(vls1,newcol) #added to existing data with global median
normalized numbers.



nvls1prot-split(normvls1,normvls1$V2) #splits up this experiment into many
files.. one for each protein.



for(n in
names(nvls1prot))write.table(nvls1prot[[n]],file=paste(nvls1prot[[n]][,V4][1],_,
n,.TXT,sep=))  #writes these files



Then I took this output in windows explorer and moved it to a new folder.
Set working directory to that folder.





And, lifted from a help page and tweaked to my liking..



# batch import text files (files must be in working directory);
'pattern' is case-sensitive

txtfiles = list.files(pattern=*.TXT)



for (i in 1:length(txtfiles)){

  tmp = read.table(txtfiles[i])

  xyz = data.frame(tmp)

  normHL = xyz[[5]]

median[i] = median(normHL)

}





But after that, I get the following error message.



Error in median[i] = median(normHL) :

  object of type 'closure' is not subsettable



Thanks,

Adam Kustka



SEAEFVNYQVR

B5YLU3

0.226

VLS5584

LLQTEPGTR

B5YLU3

0.199

VLS5584

SEAEFVNYQVR

B5YLU3

0.216

VLS5585

LLQTEPGTR

B5YLU3

0.183

VLS5585

SEAEFVNYQVR

B5YLU3

0.266

VLS5586

FAQMAVLGFIIPEK

B5YLU3

.2

VLS5586

LLQTEPGTR

B5YLU3

0.203

VLS5586

SEAEFVNYQVR

B5YLU3

0.516

VLS5587

FAQMAVLGFIIPEK

B5YLU3

0.764

VLS5587

IEGLGWRPK

B5YLU3

.2

VLS5587

LLQTEPGTR

B5YLU3

0.338

VLS5587

LLQTEPGTR

B5YLU3

.2

VLS5587

FSCAYLVDNPR

B5YLV4

0.131

VLS5584

ITCQDPSDDFPTYR

B5YLV4

0.122

VLS5584

SPLPEDLMPEFSFR

B5YLV4

0.105

VLS5584

ITCQDPSDDFPTYR

B5YLV4

.2

VLS5585

FLEVPMYLK

B5YLV4

.2

VLS5585

ITCQDPSDDFPTYR

B5YLV4

0.113

VLS5585

ITCQDPSDDFPTYR

B5YLV4

0.112

VLS5586

FSCAYLVDNPR

B5YLV4

0.128

VLS5586

SPLPEDLMPEFSFR

B5YLV4

0.126

VLS5586

FLEVPMYLKCLDR

B5YLV4

0.406

VLS5586

LYYNVETLK

B5YLV4

0.11

VLS5586

GEDGYLTTK

B5YLV4

0.144

VLS5586

FLEVPMYLK

B5YLV4

0.134

VLS5586

ITCQDPSDDFPTYR

B5YLV4

.2

VLS5586

FSCAYLVDNPR

B5YLV4

.2

VLS5586

FKDDFFLK

B5YLV4

0.121

VLS5586

ITCQDPSDDFPTYRDLEK

B5YLV4

0.138

VLS5586

FLEVPMYLK

B5YLV4

0.123

VLS5586

CFDDAFVR

B5YLV4

0.15

VLS5586

VFFTHGMYYTGGNLVAQVK

B5YLV4

0.25

VLS5586

FKDDFFLK

B5YLV4

0.141

VLS5586

CGFDEVHAR

B5YLV4

0.108

VLS5586

YPENYNIEELPAAGQSYIHPDTYVQR

B5YLV4

0.153

VLS5587

SPLPEDLMPEFSFR

B5YLV4

0.153

VLS5587

FSCAYLVDNPR

B5YLV4

0.137

VLS5587

LYYNVETLK

B5YLV4

0.157

VLS5587

CGFDEVHAR

B5YLV4

0.145

VLS5587

FLEVPMYLK

B5YLV4

0.142

VLS5587




On Wed, Jun 18, 2014 at 9:12 AM, Adam Kustka kus...@andromeda.rutgers.edu
wrote:



 I have a dataset of peptide 15N/14N ratios from four experiments (where
 cells are grown under different conditions and were fed either 15N or 14N
 nitrate aka plant food if you are interested) and I want to normalize each
 of these ratios to the median 15N/14N value from all 6000 peptides from
 each experiment.  Then, since these ratios (from 2 or more peptides) are
 used to calculate the protein 15N/14N abundance, I want to take the median
 value of all peptides belonging to one protein to calculate the overall
 protein 15N/14N abundance within that experiment.



 I’ve managed to break the data set into small pieces (by protein and by
 experiment), which will lead to about 500 observations.



 A dummy

[R] a workaround for indexing a function?

2014-06-18 Thread Adam Kustka 
I have a dataset of peptide 15N/14N ratios from four experiments (where
cells are grown under different conditions and were fed either 15N or 14N
nitrate aka plant food if you are interested) and I want to normalize each
of these ratios to the median 15N/14N value from all 6000 peptides from
each experiment.  Then, since these ratios (from 2 or more peptides) are
used to calculate the protein 15N/14N abundance, I want to take the median
value of all peptides belonging to one protein to calculate the overall
protein 15N/14N abundance within that experiment.



I’ve managed to break the data set into small pieces (by protein and by
experiment), which will lead to about 500 observations.



A dummy – small – dataset could look like this (below), where V1 lists the
peptides that make up a protein, V2 is the protein ID, V3 is the metric of
interest (the 15N/14N ratio of each peptide), and V4 indicates which
experiment was run.



The stumbling block here is that I cannot index the median function.



Here is what I have done so far.



y-read.table(“nameoffile.txt”)



h-split(y,y$V4)



for(n in names(h))

write.table(h[[n]], 
file=paste(y[[n]][,”V4”][4],”_”,n,”.TXT”,sep=””))



Then I (not elegantly but OK with brute force method for four files) went
into each file and calculated the median





vls1-read.table(“VLS5584_VLS5584.TXT”)  # for example, but did this four
times for each file



newcol=vls1[,3]/median(vls1[,3])



normvls1=cbind(vls1,newcol)



nvls1prot-split(normvls1,normvls1$V2)



for(n in
names(nvls1prot))write.table(nvls1prot[[n]],file=paste(nvls1prot[[n]][,V4][1],_,
n,.TXT,sep=))



Then I took this output in windows explorer and moved it to a new folder.
Set working directory to that folder.



And, lifted from a help page and tweaked to my liking..

for (i in 1:length(txtfiles)){

  tmp = read.table(txtfiles[i])

  xyz = data.frame(tmp)

  normHL = xyz[[5]]

median[i] = median(normHL)

}





But after that, I get the following error message.



Error in median[i] = median(normHL) :

  object of type 'closure' is not subsettable



Thanks,

Adam Kustka



SEAEFVNYQVR

B5YLU3

0.226

VLS5584

LLQTEPGTR

B5YLU3

0.199

VLS5584

SEAEFVNYQVR

B5YLU3

0.216

VLS5585

LLQTEPGTR

B5YLU3

0.183

VLS5585

SEAEFVNYQVR

B5YLU3

0.266

VLS5586

FAQMAVLGFIIPEK

B5YLU3

.2

VLS5586

LLQTEPGTR

B5YLU3

0.203

VLS5586

SEAEFVNYQVR

B5YLU3

0.516

VLS5587

FAQMAVLGFIIPEK

B5YLU3

0.764

VLS5587

IEGLGWRPK

B5YLU3

.2

VLS5587

LLQTEPGTR

B5YLU3

0.338

VLS5587

LLQTEPGTR

B5YLU3

.2

VLS5587

FSCAYLVDNPR

B5YLV4

0.131

VLS5584

ITCQDPSDDFPTYR

B5YLV4

0.122

VLS5584

SPLPEDLMPEFSFR

B5YLV4

0.105

VLS5584

ITCQDPSDDFPTYR

B5YLV4

.2

VLS5585

FLEVPMYLK

B5YLV4

.2

VLS5585

ITCQDPSDDFPTYR

B5YLV4

0.113

VLS5585

ITCQDPSDDFPTYR

B5YLV4

0.112

VLS5586

FSCAYLVDNPR

B5YLV4

0.128

VLS5586

SPLPEDLMPEFSFR

B5YLV4

0.126

VLS5586

FLEVPMYLKCLDR

B5YLV4

0.406

VLS5586

LYYNVETLK

B5YLV4

0.11

VLS5586

GEDGYLTTK

B5YLV4

0.144

VLS5586

FLEVPMYLK

B5YLV4

0.134

VLS5586

ITCQDPSDDFPTYR

B5YLV4

.2

VLS5586

FSCAYLVDNPR

B5YLV4

.2

VLS5586

FKDDFFLK

B5YLV4

0.121

VLS5586

ITCQDPSDDFPTYRDLEK

B5YLV4

0.138

VLS5586

FLEVPMYLK

B5YLV4

0.123

VLS5586

CFDDAFVR

B5YLV4

0.15

VLS5586

VFFTHGMYYTGGNLVAQVK

B5YLV4

0.25

VLS5586

FKDDFFLK

B5YLV4

0.141

VLS5586

CGFDEVHAR

B5YLV4

0.108

VLS5586

YPENYNIEELPAAGQSYIHPDTYVQR

B5YLV4

0.153

VLS5587

SPLPEDLMPEFSFR

B5YLV4

0.153

VLS5587

FSCAYLVDNPR

B5YLV4

0.137

VLS5587

LYYNVETLK

B5YLV4

0.157

VLS5587

CGFDEVHAR

B5YLV4

0.145

VLS5587

FLEVPMYLK

B5YLV4

0.142

VLS5587

[[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.

Re: [R] a workaround for indexing a function?

2014-06-18 Thread David Winsemius 
See this?

`[[alternative HTML version deleted]]`

Means your efforts at including data have been sabotaged by failing to read the 
Posting guide and send plain text.

Then this line:median[i] = median(normHL)

Gets you:
 Error in median[i] = median(normHL) :
 
  object of type 'closure' is not subsettable

Were you under the impression that assignment to an indexed vector with a name 
would succeed when the vector had not already been pre-defined? R was 
interpreting that as assignment to an object named 'median' which it was able 
to find. The error was thrown because the located object is a function (aka 
closure).

Better would be to chose a more specific object name and not one shared by a 
regular function. That also means you would have gotten the same error with 
objects named `df` (the density of the F distribution), `dt` (the 
t-distribution), `c` (the concatenation function), `C` (the contrasts 
function), `D` (the derivative function).. getting the idea that using one 
or two letter names might be fraught with confusion?

Try using 

 nor_med - numeric(0)  # before the loop and then in the loop use:

  nor_med[i] = median(normHL)

-- 
david.

On Jun 18, 2014, at 10:26 AM, Adam Kustka wrote:

 I noticed a missing line in the code associated with my question.  I've
 re-supplied the question now with that line.
 
 Sorry for the trouble,
 Adam
 
 
 
 
 
 I have a dataset of peptide 15N/14N ratios from four experiments (where
 cells are grown under different conditions and were fed either 15N or 14N
 nitrate aka plant food if you are interested) and I want to normalize each
 of these ratios to the median 15N/14N value from all 6000 peptides from
 each experiment.  Then, since these ratios (from 2 or more peptides) are
 used to calculate the protein 15N/14N abundance, I want to take the median
 value of all peptides belonging to one protein to calculate the overall
 protein 15N/14N abundance within that experiment.
 
 
 
 I’ve managed to break the data set into small pieces (by protein and by
 experiment), which will lead to about 500 observations.
 
 
 
 A dummy – small – dataset could look like this (below), where V1 lists the
 peptides that make up a protein, V2 is the protein ID, V3 is the metric of
 interest (the 15N/14N ratio of each peptide), and V4 indicates which
 experiment was run.
 
 
 
 The stumbling block here is that I cannot index the median function.
 
 
 
 Here is what I have done so far.
 
 
 
 y-read.table(“nameoffile.txt”)
 
 
 
 h-split(y,y$V4)
 
 
 
 for(n in names(h))
 
 write.table(h[[n]], file=paste(y[[n]][,”V4”][4],”_”,n,”.TXT”,sep=””))
 
 
 
 Then I (not elegantly but OK with brute force method for four files) went
 into each file and calculated the median
 
 
 
 
 
 vls1-read.table(“VLS5584_VLS5584.TXT”)  # for example, but did this four
 times for each file
 
 
 
 newcol=vls1[,3]/median(vls1[,3]) #make a new column of 15N/14N data now
 normalized to median value… here this is shown for one of four experiments.
 
 
 
 
 normvls1=cbind(vls1,newcol) #added to existing data with global median
 normalized numbers.
 
 
 
 nvls1prot-split(normvls1,normvls1$V2) #splits up this experiment into many
 files.. one for each protein.
 
 
 
 for(n in
 names(nvls1prot))write.table(nvls1prot[[n]],file=paste(nvls1prot[[n]][,V4][1],_,
 n,.TXT,sep=))  #writes these files
 
 
 
 Then I took this output in windows explorer and moved it to a new folder.
 Set working directory to that folder.
 
 
 
 
 
 And, lifted from a help page and tweaked to my liking..
 
 
 
 # batch import text files (files must be in working directory);
 'pattern' is case-sensitive
 
 txtfiles = list.files(pattern=*.TXT)
 
 
 
 for (i in 1:length(txtfiles)){
 
  tmp = read.table(txtfiles[i])
 
  xyz = data.frame(tmp)
 
  normHL = xyz[[5]]
 
median[i] = median(normHL)
 
 }
 
 
 
 
 
 But after that, I get the following error message.
 
 
 
 Error in median[i] = median(normHL) :
 
  object of type 'closure' is not subsettable
 
 
 
 Thanks,
 
 Adam Kustka
 
 
 
 SEAEFVNYQVR
 
 B5YLU3
 
 0.226
 
 VLS5584
 
 LLQTEPGTR
 
 B5YLU3
 
 0.199
 
 VLS5584
 
 SEAEFVNYQVR
 
 B5YLU3
 
 0.216
 
 VLS5585
 
 LLQTEPGTR
 
 B5YLU3
 
 0.183
 
 VLS5585
 
 SEAEFVNYQVR
 
 B5YLU3
 
 0.266
 
 VLS5586
 
 FAQMAVLGFIIPEK
 
 B5YLU3
 
 .2
 
 VLS5586
 
 LLQTEPGTR
 
 B5YLU3
 
 0.203
 
 VLS5586
 
 SEAEFVNYQVR
 
 B5YLU3
 
 0.516
 
 VLS5587
 
 FAQMAVLGFIIPEK
 
 B5YLU3
 
 0.764
 
 VLS5587
 
 IEGLGWRPK
 
 B5YLU3
 
 .2
 
 VLS5587
 
 LLQTEPGTR
 
 B5YLU3
 
 0.338
 
 VLS5587
 
 LLQTEPGTR
 
 B5YLU3
 
 .2
 
 VLS5587
 
 FSCAYLVDNPR
 
 B5YLV4
 
 0.131
 
 VLS5584
 
 ITCQDPSDDFPTYR
 
 B5YLV4
 
 0.122
 
 VLS5584
 
 SPLPEDLMPEFSFR
 
 B5YLV4
 
 0.105
 
 VLS5584
 
 ITCQDPSDDFPTYR
 
 B5YLV4
 
 .2
 
 VLS5585
 
 FLEVPMYLK
 
 B5YLV4
 
 .2
 
 VLS5585
 
 ITCQDPSDDFPTYR
 
 B5YLV4
 
 0.113
 
 VLS5585
 
 ITCQDPSDDFPTYR
 
 B5YLV4
 
 0.112
 
 VLS5586
 
 FSCAYLVDNPR
 
 B5YLV4
 
 0.128
 
 VLS5586
 
 SPLPEDLMPEFSFR
 
 B5YLV4
 
 0.126
 
 VLS5586