[R] Unable to extract gene list from chromosome

[David Winsemius]

On 4/8/21 3:42 PM, pooja sinha wrote:
> Hi David,
>
> Sorry I forgot to attach the file. Now it's attached.


Now when I go back and check the values of the setup variables after 
seeing an error on the last call,

Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = 
fullXmlQuery,  :
   Query ERROR: caught BioMart::Exception::Database: Error during query 
execution: You have an error in your SQL syntax; check the manual that 
corresponds to your MySQL server version for the right syntax to use 
near 'AND (main.seq_region_end_1020 >= '15108600' OR 
main.seq_region_end_1020 >= '9115' at line 1

I now notice:


AT_AC_Gene$chr

#NULL

Changing that to AT_AC_Gene$Chromosome_number gets at least a startup 
message from the server:

Batch submitting query 
[==>-------------------------------------------------------------------] 
5% eta:  1m

Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = 
fullXmlQuery,  :
   Query ERROR: caught BioMart::Exception::Database: Error during query 
execution: You have an error in your SQL syntax; check the manual that 
corresponds to your MySQL server version for the right syntax to use 
near 'AND (main.seq_region_end_1020 >= '15108600' OR 
main.seq_region_end_1020 >= '9115' at line 1

But then I get the same error before about SQL syntax error.


Then I ran it with only complete cases and now get no error but again 
see no hits:

str(final_1)
'data.frame':    0 obs. of  6 variables:
  $ external_gene_name: logi
  $ ensembl_gene_id   : logi
  $ start_position    : logi
  $ end_position      : logi
  $ rgd_symbol        : logi
  $ chromosome_name   : logi


I also see a lot of NA's in that dataset and when I just send the first 
10 rows of the request, I get no error (but also no matches.)


So you clearly are not giving us all the data or all the code, but I'm 
finally wondering if you just don't have an data that matches teh 
external datasets in your chosen "biomart". Can you offer a smaller 
dataset that you know with certainty should produce a match?


Alternatively, you might want to post this instead at the BioConductor 
mailing list. They are the people who have a better chance of spotting 
obvious errors. I've found two likely code-related errors but I'm not a 
computational biostatistician.

David

>
>
> Thanks,
> Puja
>
> On Thu, Apr 8, 2021 at 6:01 PM David Winsemius <dwinsemius using comcast.net 
> <mailto:dwinsemius using comcast.net>> wrote:
>
>
>     On 4/8/21 2:30 PM, pooja sinha wrote:
>     > Hi All,
>     >
>     > I am trying to extract gene list from chromosome number and
>     position, for
>     > that I am using biomaRt in R but I am getting error messages as
>     shown
>     > below. Also below is the code I am using for extraction.
>     >
>     > library("biomaRt")
>     > listMarts()
>     > ensembl <- useMart("ensembl")
>     > datasets <- listDatasets(ensembl)
>     > ensembl = useDataset("rnorvegicus_gene_ensembl",mart=ensembl)
>     > AT_AC_Gene <-
>     read.csv("AT-AC-methylkit_biomart-4-7-21.csv",header=T)
>
>
>     #--- a this point I get
>
>     Error in file(file, "rt") : cannot open the connection
>     In addition: Warning message:
>     In file(file, "rt") :
>        cannot open file 'AT-AC-methylkit_biomart-4-7-21.csv': No such
>     file
>     or directory
>
>     > attributes <-
>     >
>     c("external_gene_name","ensembl_gene_id","start_position","end_position","rgd_symbol","chromosome_name")
>     > filters <- c("chromosome_name","start","end")
>     > values <- list(AT_AC_Gene$chr,AT_AC_Gene$start,AT_AC_Gene$end)
>     > final_1 <- getBM(attributes=attributes, filters=filters,
>     values=values,
>     > mart=ensembl)
>     >
>     > The code runs well without any error but the final1 output has 0
>     > observations of 6 variables. Why?
>     >
>     > Can anyone help me with this?
>
>
>     You are more likely to get a useful response on the BioC mailing
>     list.
>     It appears you have a dependenciy of a csv file that you have not
>     told
>     us about.
>
>
>     -- 
>
>     David
>
>     >
>     >
>     > Thanks,
>     >
>     > Puja
>     >
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>     >
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