Thank you David - you put me into right direction. Back to normal, problem sorted. I've missed a single quote in 'annot' data when I imported it from file using read.table function with the default 'quote' argument. quote="\"" did the trick.
Many thanks -Igor On Wed, 2012-09-19 at 14:55 -0700, David Winsemius wrote: > 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 > ______________________________________________ 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.
