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.
