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

[Igor Chernukhin]

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...


-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