以向量为参数的RSQLite参数化查询

我不熟悉

SQL

及其语法，我无法理解如何使用

RSQLite

在

R

中的参数化查询中将多个值（例如向量或列表）传递给单个参数

我有一个两表数据库（

myTCGA

），数据来自RNASeq数据。第一个（

tcga_P

）包含一些基因样本的表达值（

FPKM

），而（

tcgaMeta

）包含这些样本的元数据信息

#tcga_P
      FPKM           Sample                 Tissue GeneName
5550 0.0633 TCGA-AB-2803-03A Acute_Myeloid_Leukemia  PLEKHN1
5551 0.2390 TCGA-AB-2805-03A Acute_Myeloid_Leukemia  PLEKHN1
5552 0.0253 TCGA-AB-2806-03A Acute_Myeloid_Leukemia  PLEKHN1
5553 0.0385 TCGA-AB-2807-03A Acute_Myeloid_Leukemia  PLEKHN1
5554 0.0326 TCGA-AB-2808-03A Acute_Myeloid_Leukemia  PLEKHN1
5555 0.2836 TCGA-AB-2810-03A Acute_Myeloid_Leukemia  PLEKHN1

# tcgaMeta (only few columns)
SampleIndex         SampleID        SubjectID Tumor.Type         Sample.Type
  1           0 TCGA-01-0628-11A TCGA-01-0628         OV Solid Tissue Normal
  2           1 TCGA-01-0630-11A TCGA-01-0630         OV Solid Tissue Normal
  3           2 TCGA-01-0631-11A TCGA-01-0631         OV Solid Tissue Normal

我只想从属于特定组的样本（例如所有肺样本）的

tcga_p

中提取表达值。为此，我编写了一个如下的查询

library(DBI)
library(RSQLite)
library(data.table)

myGene <- "PLEKHN1"
myTissue <- "lung"
myCancer <- "Lung Adenocarcinoma"
selectedSamples <- dbGetQuery(myTCGA, 
     "SELECT A.*
     FROM tcga_P A 
     WHERE A.GeneName = $gene AND
           A.Sample in (SELECT B.SampleID FROM tcgaMeta B 
                WHERE B.Tissue = $tissue AND 
                      B.`Disease.TCGA.` = $cancer )
     ",param = list(gene=myGene,tissue=myTissue,cancer=myCancer))
 # from long to wide
 selectedSamplesWide <- dcast(selectedSamples,GeneName~Sample, value.var = "FPKM",fun.aggregate = sum)

我可以循环（

sapply

）通过载体中的基因，一次调用一个基因并将结果绑定在一起，但我想在sql调用中做所有事情

到目前为止我试过

WHERE A.GeneName IN ($gene)
WHERE A.GeneName IN (SELECT C.GeneName FROM $gene C)

我还尝试将

myGene

转换为

data.frame

，并将基因作为列处理。说什么都没用是多余的

---

我错过了什么？如何将参数传递给

param=list（）

？

在SQL中，具有等式的

WHERE

子句，

=

，在尝试将表达式求值为两个值时，需要一个值。但是，中带有

的
WHERE
允许多个值：

其中A.GeneName位于（'PLEKHN1'，'PSMD12'，…）

对于一个不限数量的值，考虑动态创建准备好的语句，使用<代码>粘贴>代码> +>代码>塌陷< /代码>，绑定参数值与<代码>设置名称和<代码> AS .List >：
myGene <- c("PLEKHN1", "PSMD12")
myTissue <- "lung"
myCancer <- "Lung Adenocarcinoma"

myPlaceHolders <- paste0("$gene", seq_along(myGene))

sql <- paste0("SELECT A.*
               FROM tcga_P A 
               WHERE A.GeneName IN (", paste(myPlaceHolders, collapse=", "), ") 
                 AND A.Sample in (SELECT B.SampleID 
                                  FROM tcgaMeta B 
                                  WHERE B.Tissue = $tissue 
                                    AND B.`Disease.TCGA.` = $cancer)
             ")

myGeneParams <- as.list(setNames(myGene, gsub("\\$", "", myPlaceHolders)))
paramList <- c(myGeneParams, tissue=myTissue, cancer=myCancer)

selectedSamples <- dbGetQuery(myTCGA, sql, param = myParamList)

myGene感谢您提供的解决方案和清晰的解释。我不得不避开gsub模式
gsub（\\$，“”，myPlaceHolders）
，但除此之外，它还起了作用。很高兴听到这个消息并乐于提供帮助！
myGene <- c("PLEKHN1", "PSMD12")
myTissue <- "lung"
myCancer <- "Lung Adenocarcinoma"

myPlaceHolders <- paste0("$gene", seq_along(myGene))

sql <- paste0("SELECT A.*
               FROM tcga_P A 
               WHERE A.GeneName IN (", paste(myPlaceHolders, collapse=", "), ") 
                 AND A.Sample in (SELECT B.SampleID 
                                  FROM tcgaMeta B 
                                  WHERE B.Tissue = $tissue 
                                    AND B.`Disease.TCGA.` = $cancer)
             ")

myGeneParams <- as.list(setNames(myGene, gsub("\\$", "", myPlaceHolders)))
paramList <- c(myGeneParams, tissue=myTissue, cancer=myCancer)

selectedSamples <- dbGetQuery(myTCGA, sql, param = myParamList)