[BioC] problem with function
cstrato
cstrato at aon.at
Sat Dec 18 15:40:09 CET 2010
You need to do:
cumulMetric <- function(deMirPresGenes, deMirs){
fc <- deMirs
fcVector <- as.numeric(with (fc, FC[match(deMirPresGenes[,4], Probe)] ) )
metric <- fcVector * as.numeric(deMirPresGenes[,11])
geneMetric <- as.data.frame(cbind(deMirPresGenes[,2], as.numeric(metric)))
colnames(geneMetric) <- c('y', 'x')
listMetric <- unstack(geneMetric, x ~ y)
listMetric <- as.data.frame(sapply(listMetric,sum)) #returns a dataframe
colnames(listMetric) <- c('cumulMetric')
return(listMetric)
}
Regards
Christian
On 12/17/10 11:52 PM, Iain Gallagher wrote:
> 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
>>>>>>>>
>>>>>>>
>>>>>>>
>>>> _______________________________________________
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>>>>>>>
>>>>>>
>>>>>
>>>>>
>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
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>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>
>>>
>>
>
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