On 02/13/2010 07:17 AM, David Winsemius wrote: > > On Feb 13, 2010, at 10:09 AM, Martin Morgan wrote: > >> 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 ? >> >> > > Would that be: > > sapply(!is.na(test.goP), getSYMBOL, "hgu95av2")
actually, sapply(test.goP[!is.na(test.goP)], getSYMBOL, "hgu95av2") ;). Martin > > ? > >> >>> >>> In addition to the above suggestions ... post on the correct list? >> >> http://bioconductor.org/ >> >> Martin >> >>> >>>> -- > > >> Phone: (206) 667-2793 > > David Winsemius, MD > Heritage Laboratories > West Hartford, CT > -- 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.
