[BioC] problem with function

Iain Gallagher iaingallagher at btopenworld.com
Fri Dec 17 23:52:49 CET 2010


ok... done. Not really any further forward here.

print statements after creating fcVector, metric and geneMetric (see output below). They all look ok in terms of structure and length. But the error persists and listMetric is not made?!?! Odd.

I have added some comments to the output below.

> tf2<-cumulMetric(tf1, deMirs$up)#deMirs$up is a dataframe (see prev posts)
[1] 2.63 2.63 3.13 2.63 3.13 2.74 # print fcVector - looks ok
[1] -0.35505 -0.34979 -1.03290 -1.22558 -0.61348 -0.86584 # print metric - looks ok
[1] 1045 # lengthof metric - is correct
     sym      metric    # print geneMetric - looks ok
[1,] "AAK1"   "-0.35505"
[2,] "ABCA1"  "-0.34979"
[3,] "ABCA2"  "-1.0329" 
[4,] "ABCB10" "-1.22558"
[5,] "ABCE1"  "-0.61348"
[6,] "ABCF3"  "-0.86584"
[1] 1045 # nrow of geneMetric - is correct
Error in eval(expr, envir, enclos) : object 'geneMetric' not found
> 

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, 22:38
> At the moment I have no idea, but
> what I would do in this case is to put 
> print() statements after each line to see where it fails.
> 
> Christian
> 
> On 12/17/10 10:59 PM, Iain Gallagher wrote:
> > 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
> >>>>>>
> >>>>>
> >>>>>
> >> _______________________________________________
> >>>>> Bioconductor mailing list
> >>>>> Bioconductor at r-project.org
> >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>>>
> >>>>
> >>>
> >>>
> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor at r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>
> >>
> >
>



More information about the Bioconductor mailing list