[BioC] the function subset inside a function

[Mark Robinson]

Lana.

Couple things.

1. Perhaps you want to be using the 'subset' argument, not the  
'select' argument in the subset command, according to the help on the  
subset command:

---------
Arguments:

        x: object to be subsetted.

   subset: logical expression indicating elements or rows to keep:
           missing values are taken as false.

   select: expression, indicating columns to select from a data frame.

     drop: passed on to '[' indexing operator.
---------

Replace:

lapply(LI, subset, select=cov[[i]])

with:

lapply(LI, FUN=subset, subset=cov[[i]])

but ....

2. The object LI, which you are calling lapply on, is never defined in  
your example below, so I could be misleading you.  Perhaps you could  
give more details.

Mark






On 04/07/2008, at 9:02 AM, Lana Schaffer wrote:

> Hi,
> I am using this subset statement and it works outside a function.
> LIS[[i]]<- lapply(LI, subset, select=cov[[i]]) However, wrapped  
> inside a
> function this statement produces the same values for every (which is
> always LIS[[1]]) which is only the first subset of LI.
> Does anyone know why is not working correctly inside a function?
>
> ff = factor(covariate)
> nLev <- nlevels(ff)
> cov <- vector(mode="list",length=nLev)
> for (gp in 1:nLev) {
> cov[[gp]] <- covariate == levels(ff)[gp]  }
>
> LIS <- vector(mode="list",length=nLev)
> #if (SINGLE == T ) LIS[[1]] <- LI else {} for (i in 1:nLev)
> LIS[[i]]<- lapply(LI, subset, select=cov[[i]])
>
>
> -----Original Message-----
> From: Lana Schaffer
> Sent: Thursday, July 03, 2008 3:44 PM
> To: 'bioconductor at stat.math.ethz.ch'
> Subject: the function subset inside a function
>
> Hi,
> I have successfully applied the subset function on a list.  However,
> inside a function the subset did not work.  Has anyone else run into
> this problem?
>
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu
>
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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: 03 9345 2628
f: 03 9347 0852