Dear Group,
I am using biomaRt to retrieve the flanking region from the TSS. I use
the below statement for retrieving the 1000 bp upstream region from
the TSS for yeast organism.
seq=getSequence(id="R0010W",type="ensembl_gene_id",seqType="coding_gen
e_flank",upstream=1000,mart
= mart);
Now my question is if the TSS is on reverse strand and I would like to
retrive the 1000 bp upstream region what should be my command ????
Below is the command that I used..
seq=getSequence(id="R0020C",type="ensembl_gene_id",seqType="coding_gen
e_flank",downstream=1000,mart
= mart);
Please let me know if I am doing it the right way...
Thanks,
Kishor
Hello,
I'm preparing a custom cdf for a custom SNP/CNV array. However,without
success. Could someone suggest what might cause source this error?
Thanks,
Ania Lorenc
Parsing file: MOUSEDIVm520650.CDF...
Getting SNP probes...
Organizing PM probes for SNPs...
Getting SNP information...
Organizing PM probes for CNVs...
Getting sequences for SNPs...
Getting sequences for CNVs...
Merging sequence information for SNPs...
Merging sequence information for CNVs...
Creating Biostrings objects...
Error in .charToXString(basetype, x, solved_SEW) : key 32 not in
lookup
table
Calls: makePdInfoPackage ... XStringSet -> .charToXStringSet ->
.charToXString -> .Call
In addition: Warning messages:
1: In rm(cols, ok, colsOut, seq) : object 'ok' not found
2: In rm(cols, ok, colsOut, seq) : object 'ok' not found
sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] pdInfoBuilder_1.14.1 oligo_1.14.0 oligoClasses_1.12.1
[4] affxparser_1.22.0 RSQLite_0.9-3 DBI_0.2-5
[7] Biobase_2.10.0 R.utils_1.5.7 R.oo_1.7.4
[10] R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] Biostrings_2.18.0 IRanges_1.8.2 affyio_1.18.0
[4] preprocessCore_1.12.0 splines_2.12.0
>
loaded via a namespace (and not attached):
[1] tools_2.12.0
