On 02/13/2010 06:21 AM, David Winsemius wrote: > > On Feb 13, 2010, at 3:18 AM, Sahil Seth wrote: > >> Hi, >> I have been trying to find a solution to this issue, but have not been >> able >> to so ! >> I am trying to use sapply on the function getSYMBOL, > > The annotate package is from BioConductor. > >> an extract from the list is: >>> test.goP[13:14] >> $`GO:0000050` >> IEA IEA IEA IEA TAS TAS TAS >> IEA >> "5270753" "5720725" "1690128" "4850681" "110433" "2640544" "4900370" >> "1430280" >> IEA NAS TAS IEA >> "6110044" "1170615" "6590546" "1690632" >> >> $`GO:0000052` >> [1] NA >> >> goG=sapply(test.goP,getSYMBOL,data="hgu95av2") > > I was a bit surprised to see a data= argument to sapply. That didn't > seem typical but perhaps I am not aware of all the tricks available.
> args(sapply) function (X, FUN, ..., simplify = TRUE, USE.NAMES = TRUE) The ... arguments are passed to FUN. Here FUN is getSYMBOL > args(getSYMBOL) function (x, data) so data="hgu95av2" is used in each application of getSYMBOL. This could have been written as sapply(test.goP, getSYMBOL, "hgu95av2") using positional matching to getSYMBOL's arguments. A 'trick' that is sometimes useful is to use named arguments to force the apply to vary the second (or other) argument, rather than the first. >> error: "Error in .checkKeysAreWellFormed(keys) : >> keys must be supplied in a character vector with no NAs " >> In this the 14th element has missing values, thus getSYMBOL raises >> issues. > > The way this is being displayed makes me think you are processing a list > with named elements. You should use str to determine what test.goP > really is. Then you will have a better idea what functions would be > appropriate. you may want to compose a function to go with the sapply > loop that omots the NA's: > > ?na.omit > > You should also post the results of dput or dump on the test objects you > are working with. That way the list readers can also get access to that > information. >> >> GetSYMBOL has to be given a char array, so a simple solution is infact to >> delete the missing elements from the list. >> >> I have been trying to find a solution for it, but in vain: >> tried: completecases(goP), na.omit(goP) and several other things. >> >> Any suggestions please ? sapply(is.na(test.goP), getSYMBOL, "hgu95av2") > > In addition to the above suggestions ... post on the correct list? http://bioconductor.org/ Martin > >> -- > > David Winsemius, MD > Heritage Laboratories > West Hartford, CT > > ______________________________________________ > 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. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ______________________________________________ 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.
