Hi Jim - Thank you for your reply. -----------------------------8<------------------------------------ > str(annot) 'data.frame': 6895 obs. of 4 variables: $ id : int 231803 231804 231805 231810 231811 231816 231818 177697 223131 231823 ... $ kogdefline : Factor w/ 1898 levels "17 beta-hydroxysteroid dehydrogenase type 3, HSD17B3",..: 1633 693 704 1627 1042 507 1870 1448 730 185 ... $ kogClass : Factor w/ 26 levels "","Amino acid transport and metabolism ",..: 26 4 24 20 18 24 10 22 25 6 ... $ kogGroup : Factor w/ 5 levels "","CELLULAR PROCESSES AND SIGNALING",..: 3 4 2 2 2 2 2 3 3 2 ...
> str(statdata) 'data.frame': 3887 obs. of 8 variables: $ id : chr "267533" "246792" "271961" "237478" ... $ baseMean : num 288 519 309 189 341 ... $ baseMeanA : num 574 1025 617 375 661 ... $ baseMeanB : num 1.392 13.592 0.535 2.23 21.621 ... $ foldChange : num 0.002426 0.013258 0.000866 0.00594 0.032733 ... $ log2FoldChange: num -8.69 -6.24 -10.17 -7.4 -4.93 ... $ pval : num 2.82e-104 1.70e-94 4.82e-81 1.63e-79 6.62e-78 ... $ padj : num 7.31e-100 2.20e-90 4.16e-77 1.06e-75 3.43e-74 ... - attr(*, "na.action")=Class 'omit' Named int [1:1235] 17 18 20 22 31 33 39 43 44 45 ... .. ..- attr(*, "names")= chr [1:1235] "NA" "NA.1" "NA.2" "NA.3" ... > str(extra) 'data.frame': 3887 obs. of 3 variables: $ kogdefline: chr NA NA NA NA ... $ kogClass : chr NA NA NA NA ... $ kogGroup : chr NA NA NA NA ... -------------------------8<---------------------------- Also I tried "stringsAsFactors = FALSE", it doesn't seem to make any difference. -Igor On Wed, 2012-09-19 at 13:36 -0400, jim holtman wrote: > It would also be helpful if you could provide the output of 'str' for > all the objects that you are using. > > e.g., str(statdata) str(extra) > > > Also in creating your data.frame, use "stringsAsFactors = FALSE": > > extra = data.frame(kogdefline=rep(NA,n) > , kogClass = rep(NA,n) > , kogGroup = rep(NA,n) > , stringsAsFactors = FALSE > ) > > On Wed, Sep 19, 2012 at 12:12 PM, Igor <ig...@essex.ac.uk> 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 > > --------------------------------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 > > > > ______________________________________________ > > 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. > > ______________________________________________ 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.
