[BioC] R sqllite referencing columns with :1 heading

barry [guest] guest at bioconductor.org
Fri Jun 21 21:52:50 CEST 2013

  THis is more an sqllite question, however someone may know the answer here.
I am using sqllite to look at cummerbund tables.  When I do a self join the duplicate columns have a :1 suffix.   I can't seem to reference these columns in further sqllite command using the :1 notation.  I've tried to quote the column names, but I aways get a error.  Does anyone know how to reference these columns?

This code fails(even without quoting A:p_value:1.

 -- output of sessionInfo(): 

m1<-"CREATE TABLE r1 as SELECT * INTO r1 FROM geneExpDiffData A INNER JOIN geneExpDiffData B ON A.sample_2 = B.sample_2 WHERE (A.gene_id = B.gene_id) and (A.sample_1 = 'q1') and (B.sample_1 = 'q2') and (A.sample_2 = 'q3') and (A.p_value < 0.1) and (B.p_value < 0.1))"
#don't know how to specify A.p_value:1 maybe
 m2<-'SELECT A.gene_id, A.p_value, "A.p_value:1", B.p_value FROM r1 A INNER JOIN geneExpDiffData B ON A.gene_id = B.gene_id  WHERE (B.sample_1 = "q1") and (B.sample_2 = "q2") and (B.p_value > 0.1)'

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