Question

下面显示的代码用于计算不同基因列表的超几何分布。但是，出现错误，表明二进制运算符有一个非数字参数。有什么想法需要改变吗？

   #-------------------------------------------------------------------------------
    # Hypergeometric p values
    #-------------------------------------------------------------------------------
    # Set up empty matrix
    # ....

    hypergeo <- function(white.drawn, white, black, drawn, do.log=FALSE) {
      # Info: http://digitheadslabnotebook.blogspot.com/2011/02/using-r-for-introductory-statistics_21.html
      # dhyper(q, m, n, k, log = FALSE)
      #        q = number of successes; "white balls drawn" (here: number of genes that overlap)
      #        m + n = N ; N = total number of genes
      #        m = "white balls in urn"; total number of TF-bound genes
      #        n = "black balls in urn"; total number of genes NOT bound by the TF
      #        k = "number of balls drawn from urn"; sample size
      if (white < 1) {return(NA)}
      p <- phyper(white.drawn-1, white, black, drawn, lower.tail = FALSE, log.p=do.log)
      return(p)
    } # end: hypergeo

    y <- rep(NA, x)
    mx.p <- matrix(y, ncol=length(gene.lists))
    mx.p

    row.names(mx.p) <- sapply(filelist, basename) %>% stringr::str_remove('.txt$')
    colnames(mx.p) <- sapply(filelist, basename) %>% stringr::str_remove('.txt$')
    mx.p



#-------------------------------------------------------------------------------
    # loop to work our hypergeometric distribution
    #-------------------------------------------------------------------------------
    for (i in seq_along(gene.lists)) {
      g1 <- gene.lists[[i]]
      for (j in seq_along(gene.lists)) {
        g2 <- gene.lists[[j]]
        a <- intersect(g1,g2)
        b <- length(a)
        balls.white <- length(g1)
        balls.black <- 31253 - length(g1)
        balls.white.drawn <- length(intersect(g1,g2))
        balls.drawn <- length (g2)
        balls.total <- 31253
        p <- hypergeo(white.drawn = balls.white.drawn,
                      white = balls.white,
                      black = balls.black,
                      drawn =balls.drawn, do.log = FALSE)

      }
    }

Answer 1

在代码中，您定义balls.white.drawn <- intersect(g1, g2)。这两个集合的交集通常不是单个数字，而是一个向量（在您的情况下是基因的向量）。我的感觉是，您希望在g1和g2的交点中的元素的 number ，因此，您想要balls.white.drawn <- length(intersect(g1, g2))，尽管这已经是您要定义的a。

white.drawn中的错误-1：二进制运算符的非数字参数

1 个答案: