[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
> >>>>
> >>>
> >>>
> _______________________________________________
> >>> 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