i have this genes from saccharomyces cerevisiae
genes <- c("YAL002W", "YAL003W","YAL004W", "YAL005C","YAL007C","YAL008W","YAL009W","YAL010C", "ETS1-1", "ETS1-2","ETS2-1","ETS2-2", "HRA1", "ICR1", "IRT1", "ITS1-1")
and I have tried this
my.simbols <- genes
sc <- org.Sc.sgd.db select(sc, keys = my.simbols, columns = c("ENTREZID", "SYMBOL", "GENEID"), keytype = "SYMBOL")
and this is the ouput error
Error in testForValidKeytype(x, keytype) : Invalid keytype: SYMBOL. Please use the keytypes method to see a listing of valid arguments.
Hi cesarihv7,
I think you can use:
select(
sc,
keys = my.simbols,
columns = c("ENTREZID", "GENENAME", "SGD")
)
Which returns:
> select(
+ sc,
+ keys = my.simbols,
+ columns = c("ENTREZID", "GENENAME", "SGD")
+ )
'select()' returned 1:1 mapping between keys and columns
ORF ENTREZID GENENAME SGD
1 YAL002W 851261 VPS8 S000000002
2 YAL003W 851260 EFB1 S000000003
3 YAL004W <NA> <NA> S000002136
4 YAL005C 851259 SSA1 S000000004
5 YAL007C 851226 ERP2 S000000005
6 YAL008W 851225 FUN14 S000000006
7 YAL009W 851224 SPO7 S000000007
8 YAL010C 851223 MDM10 S000000008
9 ETS1-1 9164941 ETS1-1 S000029717
10 ETS1-2 9164933 ETS1-2 S000029707
11 ETS2-1 9164936 ETS2-1 S000029718
12 ETS2-2 9164942 ETS2-2 S000029713
13 HRA1 9164866 HRA1 S000119380
14 ICR1 9164906 ICR1 S000132612
15 IRT1 23547381 IRT1 S000178119
16 ITS1-1 9164938 ITS1-1 S000029715
And you can use columns(org.Sc.sgd.db) to check what fields are available.
lot of thanks SMK ,I think that I have to read the org.Sc.sgd.db manual becaues by can see is a basic problem, lot of thanks. However, in the column(org.Sc.sgd.db) I can't see the transcript lenght option. Can you help me to get the transcript length?
You can try biomaRt:
> library("biomaRt")
> ensembl <- useMart("ensembl", dataset = "scerevisiae_gene_ensembl")
> getBM(
+ attributes = c("ensembl_gene_id", "transcript_length", "external_gene_name", "entrezgene"),
+ filters = "ensembl_gene_id",
+ values = genes,
+ mart = ensembl
+ )
ensembl_gene_id transcript_length external_gene_name entrezgene
1 ETS1-1 700 NA
2 ETS1-2 700 NA
3 ETS2-1 211 NA
4 ETS2-2 211 NA
5 HRA1 564 NA
6 ICR1 3199 NA
7 IRT1 1489 NA
8 ITS1-1 361 NA
9 YAL002W 3825 VPS8 851261
10 YAL003W 621 EFB1 851260
11 YAL004W 648 NA
12 YAL005C 1929 SSA1 851259
13 YAL007C 648 851226
14 YAL008W 597 851225
15 YAL009W 780 851224
16 YAL010C 1482 MDM10 851223
Available attributes can be shown using listAttributes(ensembl).
hi again, when I closed session in R I tried the command again
select(sc, keys = my.simbols, columns = c("ENTREZID", "GENENAME", "GO", "PATH"))
and got the following result: 'select()' returned 1:many mapping between keys and columns
and instead of having 7000 genes with this result, I have more than 100,000 and that is incorrect
help please
You can type:
keytypes(sc)
and
columns(sc)
to know what kind of information you can get from this AnnotationDb object.
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lot of thanks SMK and ricket.woo,I think that I have to read the org.Sc.sgd.db manual becaues by can see is a basic problem, lot of thanks. However, in the column(org.Sc.sgd.db) I can't see the transcript lenght option. Can you help me to get the transcript length?