Question

SELECT COUNT（DISTINCT cgi.sample_idSince）Impala不允许SET操作或select语句中的子查询，我很难弄清楚如何将列值除以返回的总行数。我的最终目标是计算每个chr：起始位置的次要等位基因频率。

我的数据结构如下：

| chr | start    | stop     | ref | allele1seq | allele2seq | sample_id | 
|  6  | 66720709 | 66720710 |  A  |      A     |     T      | 101-46-3  |
|  7  | 66720809 | 66720810 |  GG |      GA    |     GG     | 101-46-3  |

我想做类似于以下查询的事情：

WITH vars as
(SELECT cgi.chr, cgi.start, concat(cgi.chr, ':', CAST(cgi.start AS STRING)) as pos, cgi.ref, cgi.allele1seq, cgi.allele2seq,
    CASE 
        WHEN (cgi.allele1seq = cgi.ref AND cgi.allele2seq <> cgi.ref) THEN '1'  
        WHEN (cgi.allele1seq <> cgi.ref AND cgi.allele2seq = cgi.ref) THEN '1' 
        WHEN (cgi.allele1seq = cgi.ref AND cgi.allele2seq = cgi.ref) THEN '2' 
        ELSE '0' END as ma_count
    FROM comgen_variants as cgi)

SELECT vars.*, (CAST(vars.ma_count as INT)/
((SELECT COUNT(DISTINCT cgi.sample_id) from comgen_variants as cgi) * 2)) as maf
FROM vars

我想要的输出结果如下：

| chr | start    | ref | allele1seq | allele2seq | ma_count | maf |  
|  6  | 66720709 |  A  |      A     |     T      |     1    | .05 | 
|  7  | 66720809 |  GG |      GG    |     GG     |     0    |  0  |

除了找出按行计数的方法之外，我还需要按chr和pos对结果进行分组，然后计算每个备用等位基因（其中allele1seq和allele2seq不等于ref）的出现次数如上所述，按行计算;但由于计算问题，我还没有那么远。

提前感谢您的帮助。

Answer 1

看起来您可以提前计算total number of distinct sample_ids*2，然后将其用于后续查询，因为该值不会每行更改。如果值取决于行，您可能需要查看analytic/window functions available to Impala。

但是，由于它看起来不像你需要，你可以做类似以下的事情：

WITH total AS 
(SELECT COUNT(DISTINCT sample_id) * 2 AS total FROM comgen_variants)

SELECT cgi.*,
       (CASE 
          WHEN (cgi.allele1seq = cgi.ref AND cgi.allele2seq <> cgi.ref) THEN 1  
          WHEN (cgi.allele1seq <> cgi.ref AND cgi.allele2seq = cgi.ref) THEN 1 
          WHEN (cgi.allele1seq = cgi.ref AND cgi.allele2seq = cgi.ref) THEN 2
          ELSE 0 END) / total.total AS maf
FROM comgen_variants AS cgi, total;

我不确定这是次要等位基因的频率是多少;您似乎想为每个基因座选择第二个最常见的等位基因频率？

将列值除以impala中的总行数

1 个答案: