[BioC] problem with function

[cstrato]

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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