[BioC] problem with function
cstrato
cstrato at aon.at
Fri Dec 17 23:38:49 CET 2010
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
>>>>>>
>>>>>
>>>>>
>> _______________________________________________
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>>>>>
>>>>
>>>
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>>
>
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