Question

我的数据框架如下所示

SYMBOL INTENSITY1 CALL1     PVALUE1 INTENSITY2 CALL2    PVALUE2  INTENSITY3 CALL3     PVALUE3
  CCL5         NA  <NA>    0.000         NA  <NA>         NA 1125.518318     P    0.000943658
CYP2A6  141.73193     A 0.060419342   102.5146     A 0.08940508  227.369549  A    0.218983229
CYP2E1   57.67287     P 0.024710915   134.4076     P 0.000000    6.090816    A    0.040000000
  DDR1 3242.90209     P 0.000218932         NA  <NA>         NA 7015.297075  P    0.000218932
 EPHB3   78.58733     A 0.234556513   453.3487     P 0.00222774  125.238085  A    0.418069378

我使用以下代码通过Fisher方法

计算p值

Fisher.test <- function(p) {
  Xsq <- -2*sum(log(p))
  p.val <- pchisq(Xsq, df = 2*length(p), lower.tail = FALSE)
  return(c( p.value = p.val)) #
}

感谢Tim Biegeleisen

p.cols <- grep("PVALUE", names(data))
data$Fishers <- apply(data[, names(data)[p.cols]], 1, function(x) Fisher.test(x))

现在问题是行中的零条目。在第一行中，PVALUE条目为0.000, 0.00094365，如果我在Fisher.test Fisher.test`上计算c(0.000, 0.00094365) , it give the result as zero, but the correct result is 0.00094365. So i need to skip the zero entries of the rows from passing through the。

所需的输出

SYMBOL INTENSITY1 CALL1     PVALUE1 INTENSITY2 CALL2    PVALUE2  INTENSITY3 CALL3     PVALUE3        Fisher's
      CCL5       NA   <NA>    0.000        NA     <NA>         NA   1125.518318   P       0.000943658  0.000943658
      CYP2A6  141.73193 A     0.060419342 102.5146  A      0.08940508  227.369549 A       0.218983229  0.03602191
      CYP2E1  57.67287  P  0.024710915    134.4076  P      0.000000    6.090816 A       0.040000000    0.007828
      DDR1    3242.90209 P 0.000218932         NA  <NA>         NA 7015.297075    P       0.000218932  0.0000008557
      EPHB3   78.58733   A 0.234556513    453.3487   P    0.00222774  125.238085  A       0.418069378  0.00982

Answer 1

我们可以在应用Fisher.test

之前删除每行中的0个元素

apply(data[, names(data)][p.cols]], 1, function(x) Fisher.test(x[x!=0]))

在运行渔民测试时略过零条目

1 个答案: