[BioC] problem with function

[cstrato]

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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