Hi,

I have a question when using this package. Some candidate microRNA targets
seem to be missing.

Here is an example. I searched through the TargetScan website, and found
that "hsa-miR-939"
has a candidate target "CYFIP2". This gene is represented by at least one
probe "A_23_P156117".
I couldn't  find this relationship using RmiR. Don't know whether I missed
something.

I made a toy example here.

>  library(hgug4112a.db)
>  library(annotate)
>  lookUp("A_23_P156117","hgug4112a","SYMBOL")
$A_23_P156117
[1] "CYFIP2"

>  genes = data.frame(genes=c("A_23_P156117", "A_23_P352870"), expr=c(-1.3,
1.5))
>  mirna = data.frame(mirna=c("hsa-miR-939", "hsa-miR-630"), expr=c(1.1,
1.3))
>  library(RmiR)
Loading required package: RmiR.Hs.miRNA
Loading required package: RSVGTipsDevice
>  comb = read.mir(genes=genes, mirna=mirna, annotation="hgug4112a.db",
id.out="probes", at.least=1)
Error in `$<-.data.frame`(`*tmp*`, "mirCV", value = NA) :
  replacement has 1 rows, data has 0
>
> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-redhat-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] RmiR_1.2.0           RSVGTipsDevice_1.0-1 RmiR.Hs.miRNA_1.0.6
 [4] annotate_1.24.0      hgug4112a.db_2.3.6   org.Hs.eg.db_2.3.6
 [7] RSQLite_0.7-3        DBI_0.2-4            AnnotationDbi_1.8.1
[10] Biobase_2.6.1

loaded via a namespace (and not attached):
[1] xtable_1.5-6
>

Jason

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