[R] help with function

[Charles C. Berry]

On Fri, 17 Dec 2010, Iain Gallagher wrote:

> Hello List
>
> I'm moving this over from the bioC list as, although the problem I'm working on is biological, the current bottle neck is my poor understanding of R.
>
> I wonder if someone would help me with the following function.
>

Here is how I'd take it apart.

Either

  1) put browser() as the first line of the function,then feed lines to the
     browser one -by-one to see where it hangs,

  2) trace(cumulMetric) , then try to run it (much like 1, but it will
     handle feeding the lines of the function more easily)

  3) options( error = recover ), then run it till it hits the error, then
     browser thru the frames to see what is where

See

 	?browser
 	?trace
 	?recover

as background.

HTH,

Chuck

> 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(deMirPresGenes[,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
>
> although it is much longer in 'real life'.
>
> 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
>
> In an effort to debug this I have examined each object using 'print' statements (as suggested by cstrato on the bioC list).
>
> All the objects in the function up until listMetric 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 above - it is the same as deMirs)
>
>
> [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 # length of 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
>>
>
> Could someone possibly point out where I falling down.
>
> Thanks
>
> iain
>
>> 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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>

Charles C. Berry                            Dept of Family/Preventive Medicine
cberry at tajo.ucsd.edu			    UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901