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")
?
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
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