[BioC] problem with function

Iain Gallagher iaingallagher at btopenworld.com
Fri Dec 17 22:59:09 CET 2010


Hi

FC is the second column of the deMirs variable. deMirs is a dataframe with 2 columns - Probe (e.g. hsa-miR-145) and FC (e.g 1.45). Using 'with' allows me to use deMirs as an 'environment'. I thus don't have to pass FC explicitly.

Cheers

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, 20:39
> What is FC[]?  It is not passed
> to the function. Christan
> 
> On 12/17/10 8:11 PM, Iain Gallagher wrote:
> > 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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> >>>
> >>
> >
> > _______________________________________________
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> >
>



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