[BioC] problem with function

[Iain Gallagher]

Sorry.

That was a typo. In my script deMirPresGenes1[,4] is deMirPresGenes[,4].

Just to be sure I'm going about this the right way though I should say that at the moment I assign the output of another function to a variable called 'tf1' - this object is the same as the deMirPresGenes is my previous email.

This is then fed to my problem function using positional matching. 

e.g. tf2 <- cumulMetric(tf1, deMirs)

Which leads to:

Error in eval(expr, envir, enclos) : object 'geneMetric' not found

Hey ho!

i

--- On Fri, 17/12/10, cstrato <cstrato at aon.at> wrote:

> From: cstrato <cstrato at aon.at>
> Subject: Re: [BioC] problem with function
> To: "Iain Gallagher" <iaingallagher at btopenworld.com>
> Cc: "bioconductor" <bioconductor at stat.math.ethz.ch>
> Date: Friday, 17 December, 2010, 18:40
> I am not sure but I would say that
> deMirPresGenes1 does not exist.
> 
> Regards
> Christian
> 
> 
> On 12/17/10 6:42 PM, Iain Gallagher wrote:
> > Hello List
> >
> > I wonder if someone would help me with the following
> function.
> >
> > cumulMetric<- function(deMirPresGenes, deMirs){
> >     
> > #need to match position of each miR in deMirPresGenes
> with its FC to form a vector of FC in correct order
> >     fc<- deMirs
> >     fcVector<- as.numeric(with (fc,
> FC[match(deMirPresGenes1[,4], Probe)] ) )
> >
> >     #multiply fc by context score for
> each interaction
> >     metric<- fcVector *
> as.numeric(deMirPresGenes[,11])
> >     geneMetric<-
> cbind(deMirPresGenes[,2], as.numeric(metric))
> >
> >       #make cumul
> weighted score
> >     listMetric<- unstack(geneMetric,
> as.numeric(geneMetric[,2])~geneMetric[,1])
> >     listMetric<-
> as.data.frame(sapply(listMetric,sum)) #returns a dataframe
> >     colnames(listMetric)<-
> c('cumulMetric')
> >
> >     #return whole list
> >     return(listMetric)
> > }
> >
> > deMirPresGenes looks like this:
> >
> > Gene.ID   
> Gene.Symbol    Species.ID   
> miRNA    Site.type   
> UTR_start    UTR_end   
> X3pairing_contr   
> local_AU_contr   
> position_contr   
> context_score    context_percentile
> > 22848    AAK1   
> 9606    hsa-miR-183   
> 2    1546   
> 1552    -0.026   
> -0.047    0.099   
> -0.135    47
> > 19    ABCA1   
> 9606    hsa-miR-183   
> 2    1366   
> 1372    -0.011   
> -0.048    0.087   
> -0.133    46
> > 20    ABCA2   
> 9606    hsa-miR-495   
> 2    666   
> 672    -0.042   
> -0.092    -0.035   
> -0.33    93
> > 23456    ABCB10   
> 9606    hsa-miR-183   
> 3    1475   
> 1481    0.003   
> -0.109    -0.05   
> -0.466    98
> > 6059    ABCE1   
> 9606    hsa-miR-495   
> 2    1474   
> 1480    0.005   
> -0.046    0.006   
> -0.196    58
> > 55324    ABCF3   
> 9606    hsa-miR-1275   
> 3    90   
> 96    0.007   
> 0.042    -0.055   
> -0.316    94
> >
> >
> > The aim of the function is to extract a dataframe of
> gene symbols along with a weighted score from the above
> data. The weighted score is the FC column of deMirs * the
> context_score column of deMirPresGenes. This is easy peasy!
> >
> > Where I'm falling down is that if I run this function
> it complains that 'geneMetric' can't be found. Hmm - I've
> run it all line by line (i.e. not as a function) and it
> works but wrapped up like this it fails!
> >
> > e.g.
> >
> >> testF2<- cumulMetric(testF1, deMirs$up)
> > Error in eval(expr, envir, enclos) : object
> 'geneMetric' not found
> >
> > deMirs$up looks like this:
> >
> > Probe    FC
> > hsa-miR-183    2.63
> > hsa-miR-1275    2.74
> > hsa-miR-495    3.13
> > hsa-miR-886-3p    3.73
> > hsa-miR-886-5p    3.97
> > hsa-miR-144*    6.62
> > hsa-miR-451    7.94
> >
> > Could someone possibly point out where I falling
> down.
> >
> > Thanks
> >
> > i
> >
> >> sessionInfo()
> > R version 2.12.0 (2010-10-15)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > locale:
> >   [1] LC_CTYPE=en_GB.utf8   
>    LC_NUMERIC=C
> >   [3] LC_TIME=en_GB.utf8   
>     LC_COLLATE=en_GB.utf8
> >   [5] LC_MONETARY=C     
>        LC_MESSAGES=en_GB.utf8
> >   [7] LC_PAPER=en_GB.utf8   
>    LC_NAME=C
> >   [9] LC_ADDRESS=C     
>         LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics 
> grDevices utils     datasets 
> methods   base
> >
> > loaded via a namespace (and not attached):
> > [1] tools_2.12.0
> >>
> >
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>