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

[David Winsemius]

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