Hello,
I am using targetScan package for R. The function mget for targetscan.Hs.egTARGETSFULL gives an error when it stumbles upon an entrez gene id (a key) in which there is no value giving the error e.g. Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "101930100" not found. I want the function to skip the ones in which there is no corresponding value and find the values for other entrez gene ids. Do you guys know a way around this? Thanks in advance for your time.
•
written
by
alptaciroglu •
1 answer
Try using ifnotfound argument for mget function.
Following example code I used:
See if this works:
1) I saved the entrez id list above, as a text file "test"
entrezgene
1 138241
2 283349
3 101930100
4 3841
5 92703
6 653659
2) Loaded the file in R
test=read.delim2("test", header = T, stringsAsFactors = F, sep = "")
3) loaded the library
library("targetscan.Hs.eg.db")
4) executed following code without errors:
mget(as.character(test[,1]), targetscan.Hs.egTARGETS, ifnotfound = as.list(NA))
output is huge and didn't want to paste here.
5) executed following code to reproduce error:
mget(as.character(test[,1]), targetscan.Hs.egTARGETS)
Error produced:
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :value for "138241" not found
session info:
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu Wily Werewolf (development branch)
locale:
[1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8
[4] LC_COLLATE=en_IN.UTF-8 LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8
[7] LC_PAPER=en_IN.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] targetscan.Hs.eg.db_0.6.1 RSQLite_1.0.0 DBI_0.3.1
[4] AnnotationDbi_1.30.1 GenomeInfoDb_1.4.3 IRanges_2.2.9
[7] S4Vectors_0.6.6 Biobase_2.28.0 BiocGenerics_0.14.0
loaded via a namespace (and not attached):
[1] tools_3.2.2
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