Dear List,

I have a list of gene.symbol, that looks like that

>head(mylist)
$cluster.1
[1] "HSP90AB1" "INMT"     "CKB"      "NR2E1"    "ME3"      "FAM162A"
"KIRREL2" 

$cluster.2
 [1] "ENSG00000212860" "TRADD"           "C1QBP"           "KIAA1967"
"ENSG00000137379" "MAP3K3"          "TNFRSF1B"        "BAG2"
 [9] "ENSG00000212866" "RIPK3"           "EPRS"            "HSPA6"
"HSPA5"           "IKBKG"           "TBK1"            "TRAF2"
[17] "MAP3K7"          "NFKB1"           "MAP3K14"         "HSPA1A"
"MAP3K7IP2"       "HSPBP1"          "NFKB2"           "DNAJA1"
[25] "TNFRSF1A"        "TRAF3IP2"        "NFKBIA"          "HSPA9"
"ENSG00000183311" "TUBB"            "TUBA3D"          "TANK"
[33] "ENSG00000215292" "REL"             "MAP3K1"          "HSPA1B"
"HSPA8"           "NFKBIB"          "PGAM5"           "EEF1A2"
[41] "MAP3K8"          "CLTC"            "RCN2"            "MAP3K7IP1"
"RARS"            "TRAF1"           "TUBA3C"          "HSPA1L"
[49] "MYO1D"           "NOD1"            "HSP90AA2"        "CAD"
"RELB"            "AIFM1"           "TUBB2B"          "RIPK2"
[57] "CDC37"           "IKBKB"           "ERLIN1"          "RIPK1"
"TNIP2"           "STUB1"           "TUBB4"           "HSPA2"
[65] "CHUK"            "DNAJC3"          "CCDC50"          "SLC25A5"
"NFKBIE"          "AK3"             "TICAM1"          "TIMM50"
[73] "ANKRD17"         "OTUD7B"          "TNFAIP3"         "RPS27L"
"TRPC4AP"         "TUBB6"           "DNAJC6"          "PXMP2"
[81] "FLJ25006"    

$cluster.3
 [1] "ACTB"    "PFN1"    "XPO6"    "VASP"    "ZYX"     "PFN2"    "DIAPH1"
"APBB1IP" "DIAPH2"  "PARVG"   "ENAH"    "PCYT1B"  "PFN4"    "CNN2"
"NSMAF"   "PFN3"   
[17] "LMOD1"  

$cluster.4
 [1] "UBB"             "HERC3"           "KLRK1"           "ULBP1"
"RAET1E"          "MICA"            "HCST"            "ENSG00000184444"
 [9] "ENSG00000206449" "ULBP2"           "ZNF385A"         "ULBP3"
"RAET1G"         

$cluster.5
[1] "YWHAZ"    "SLAIN2"   "ZC3H13"   "C12orf51" "PGLYRP1"  "ATL3"

$cluster.6
[1] "ACTG1"   "EPS8L3"  "PARVG"   "TMSB4Y"  "B3GALT1" "UGT1A6˛


I want to extract the GO terms for every clsuter (e.g each list component)
but excluding some of them based on their evidence codes (such as IEA or
NR). The code Išm using is the following:

e2s <- toTable(org.Hs.egSYMBOL)
p <- lapply(mylist, function(x) {y <- e2s$gene_id[e2s$symbol %in% x];
return(y)})



entrezIDs <- lapply(p, function(x) {org.Hs.egGO(x)})

list.GO <- lapply(entrezIDs, function(x){toTable(x)})


With this approach I got a list of data.frames (list.GO) where I can exclude
the evidence code afterwards, however I would like to know whether any way
to exclude the evidence codes before mapping my entrez ids to GO terms.
My final aim is to calculate a semantic similarity index inside the clusters

Many thanks for the help

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] annotate_1.40.0      GO.db_2.10.1         org.Hs.eg.db_2.10.1
RSQLite_0.11.4       DBI_0.2-7            AnnotationDbi_1.24.0
Biobase_2.22.0     
 [8] BiocGenerics_0.8.0   pheatmap_0.7.7       RColorBrewer_1.0-5   plyr_1.8

loaded via a namespace (and not attached):
[1] grid_3.0.2     IRanges_1.20.5 stats4_3.0.2   tools_3.0.2    XML_3.95-0.2
xtable_1.7-1  

---
Juan Fernandez Tajes, phD
Grupo Xenomar ­ Área de Genética
Facultad de Ciencias ­ A Zapateira
Universidad de A Coruńa
Spain
Tlf - +34 981 16700
Email: Jfernandezt@udc.es
--




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