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.
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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