[R] write.table: strange output has been produced

Wed Sep 19 23:55:46 CEST 2012

On Sep 19, 2012, at 12:20 PM, Igor Chernukhin wrote:

> Hi David - 
> Thank you for your reply. You are probably right. The last 'normal' line
> doesn't have a double quote closed. There is the complete line below:
> 
> -------------------------8<------------------------------------
> "4657","159998",133.10761487064,185.450704462326,80.7645252789532,0.435504009074069,-1.19924209513405,2.75544399955331e-07,4.75176501174632e-06,"IMP-GMP specific 5-nucleotidase	Nucleotide transport and metabolism 	METABOLISM
> --------------------------8<------------------------------------
> 
> So it might be that the annotation dataset is actually the culprit. But
> it gets more complicated when I try to find find this string in the
> 'annot' object using the id value. 
> The id 159998 is present in the output from 'intersect' function:
> 
>> which(subset == 159998)
> [1] 539
> 
> It also present in statdata:
> 
>> which(statdata$id == 159998)
> [1] 1502
> 
> But I cannot find it in the 'annot' object???
> 
>> which(annot$id == 159998)
> integer(0)
> 
>> class(annot$id)
> [1] "integer"
> 
> Could it be that the annot dataset contains some illegal symbols that
> screw everything? Shall I just edit it first with 'sed' to remove
> everything except alpha-numeric before importing to R...

I find it very productive to use the count.fields function. It lets you play around with removing the comment character which you do not yet seem to have done. I find this code particularly useful:

table(count.fields(file = "fil.ext", sep="," quote="'", comment.char=""))

This would get tripped up with commas inside the double-quotes quoted strings, but I do not see any of those in the fragments your offered.

-- 
David.
> 
> 
> -Igor
> 
> 
> 
> 
> 
> 
> 
> On Wed, 2012-09-19 at 10:26 -0700, David Winsemius wrote:
>> On Sep 19, 2012, at 9:12 AM, Igor wrote:
>> 
>>> Good afternoon all -
>>> 
>>> While making a steady progress in learning R after Matlab I encountered
>>> a problem which seems to require some extra help to move over.
>>> Basically I want to merge a data from biological statistical dataset
>>> with annotation data extracted from another dataset using an 'id'
>>> crossreference and write it to report file. The first part goes
>>> absolutely fine, I have merged both data into data.frame but when I try
>>> to write it to csv file using 'write.table' it seems like it does write
>>> the 'data.frame' object but it also insert some parts from the
>>> annotation data which are not suppose to be there...
>>> There is a little snapshot of the file output below to illustrate. The
>>> upper half is fine, that's how it should be. The lower half, which is
>>> actually appears to be space-separated, not coma, obviously grabbed from
>>> the annotation dataset and is not supposed to be here.
>>> 
>>> --------------------------------8<--------------------------------------------
>>> "344","166128",126.44286392082,179.904700814932,72.9810270267088,0.40566492535281,-1.3016395254146,2.47449355237252e-07,4.2901159299567e-06,"Chitinas
>>> "18816","238247",92.5282508325735,135.981255262454,49.0752464026927,0.36089714209487,-1.47034037615176,2.5330054329543e-07,4.38862252337004e-06,"Prot
>>> "22072","222365",30.8191942806426,52.4262903365628,9.21209822472236,0.17571524068522,-2.50868876576414,2.54433836512085e-07,4.40531098485028e-06,NA,N
>>> "25062","226605",30.808007579908,50.3976662241578,11.2183489356581,0.22259659575825,-2.16749656564076,2.54934711860645e-07,4.41103467375713e-06,NA,NA
>>> "7539","247009",75.4175439970731,34.4643221134552,116.370765880691,3.37655751642533,1.75555313265164,2.60010673210741e-07,4.49585878338091e-06,NA,NA,
>>> "407","267139",425.559675915702,279.393013150954,571.72633868045,2.04631580522577,1.03302881149302,2.61074218843609e-07,4.51123710239304e-06,NA,NA,NA
>>> "26530","171300",146.80096060985,80.0063286553601,213.595592564339,2.66973370924738,1.4166958484644,2.68061220749976e-07,4.62888115991058e-06,NA,NA,N
>>> "3078","159013",34.3260176515511,52.4580790080106,16.1939562950917,0.308702808057816,-1.69570948866688,2.69104298652827e-07,4.64379716436078e-06,"40S
>>> "4657","159998",133.10761487064,185.450704462326,80.7645252789532,0.435504009074069,-1.19924209513405,2.75544399955331e-07,4.75176501174632e-06,"IMP-
>>> 
>>> 171597  171597  KOG1347 Uncharacterized membrane protein, predicted
>>> efflux pump General function prediction only    POORLY CHARACTERIZED
>>> 171658  171658  KOG4290 Predicted membrane protein  Function unknown
>>> POORLY CHARACTERIZED
>>> 171660  171660  KOG0903 Phosphatidylinositol 4-kinase, involved in
>>> intracellular trafficking and secretion  Signal transduction mechanisms
>>> CELLULAR 
>>> 171660  171660  KOG0903 Phosphatidylinositol 4-kinase, involved in
>>> intracellular trafficking and secretion  Intracellular trafficking,
>>> secretion, and
>>> 171703  171703  KOG2674 Cysteine protease required for autophagy -
>>> Apg4p/Aut2p  Cytoskeleton    CELLULAR PROCESSES AND SIGNALING
>>> 171703  171703  KOG2674 Cysteine protease required for autophagy -
>>> Apg4p/Aut2p  Intracellular trafficking, secretion, and vesicular
>>> transport   CELLU
>>> and metabolism     METABOLISM
>> 
>> This looks like the sort of thing that occurs when there is a mismatched or missing double or single quote or perhaps comment character ( "#" that terminated a line read) somewhare. The logical place to look is in the line of data just above the pathological stretch of data. You have clearly only offered a truncated version of the data, since there are many instances of lines ending without matching quotes, even one in the first line.
>> 
>> -- 
>> David.
>> 
>> 
>>> --------------------------------8<--------------------------------------------
>>> And this is a piece of code that produced this:
>>> 
>>> --------------------------------8<--------------------------------------------
>>>> n = nrow(statdata)
>>>> extra = data.frame(kogdefline=rep(NA,n), kogClass = rep(NA,n), kogGroup
>>> = rep(NA,n))
>>>> subset = intersect(statdata$id, annot$id)
>>>> MR = match(subset, annot$id)
>>>> ML = match(subset, statdata$id)
>>> 
>>>> extra[ML,1] = as.character(annot[MR,2])
>>>> extra[ML,2] = as.character(annot[MR,3])
>>>> extra[ML,3] = as.character(annot[MR,4])
>>> # strangely, if I do    
>>> # extra[ML,] = as.character(annot[MR,2:4])
>>> # it produces digits (???) instead of a string value
>>> 
>>>> mergedData = data.frame(statdata, extra)
>>>> write.table(mergedData, 'filename.csv', sep=',')
>>> --------------------------------8<--------------------------------------------
>>> 
>>> Any ideas why this is happening?
>>> 
>>> Many thanks
>>> -Igor
>> 
>> David Winsemius, MD
>> Alameda, CA, USA
>> 
> 
> -- 
> Dr I Chernukhin
> School of Biological Sciences
> University of Essex
> Wivenhoe Park
> Colchester
> Essex
> CO4 3SQ
> 

David Winsemius, MD
Alameda, CA, USA