glm 用于 R 中的多个变量

Question

我想为我的 snps 阵列建模。我可以使用以下代码一一完成。

Data$DX=as.factor(Data$DX)
univariate=glm(relevel(DX, "CON") ~ relevel(rs6693065_D,"AA"), family = binomial, data = Data)
summary(univariate)
exp(cbind(OR = coef(univariate), confint(univariate)))

如何使用循环或应用对所有其他 snps 执行此操作？ snps 是 rs6693065_D、rs6693065_A 和数百个。从上面的代码中，只有 "rs6693065_D" 将被所有其他 snps 替换。最好的祝福齐鲁尔

Answer 1

考虑开发一种通用方法来处理任何 snps。然后使用 lapply 或 sapply:

迭代传递每个 snps 列

# GENERALIZED METHOD
proc_glm <- function(snps) {
   univariate <- glm(relevel(data$DX, "CON") ~ relevel(snps, "AA"), family = binomial)

   return(exp(cbind(OR = coef(univariate), confint(univariate))))
}

# BUILD LIST OF FUNCTION OUTPUT 
glm_list <- lapply(Data[3:426], proc_glm)

如果出现 relevel:

这样的错误，请使用 tryCatch

# BUILD LIST OF FUNCTION OUTPUT 
glm_list <- lapply(Data[3:426], function(col) 
                   tryCatch(proc_glm(col), error = function(e) e))

为了构建数据框，调整方法和 lapply 调用后跟 do.call + rbind:

proc_glm <- function(col){
  # BUILD FORMULA BY STRING
  univariate <- glm(as.formula(paste("y ~", col)), family = binomial, data = Data)

  # RETURN DATA FRAME OF COLUMN AND ESTIMATES
  cbind.data.frame(COL = col,
                   exp(cbind(OR = coef(univariate), confint(univariate)))
  )
}

# BUILD LIST OF DFs, PASSING COLUMN NAMES
glm_list <- lapply(names(Data)[3:426], 
                   tryCatch(proc_glm(col), error = function(e) NA))

# APPEND ALL DFs FOR SINGLE MASTER DF
final_df <- do.call(rbind, glm_list)

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