other.oneside.pvalues {metaSeq} | R Documentation

## Optional function for non-NOISeq method

### Description

Optional function for non-NOISeq method users. P-values or probability in one-sided test in positive and negative differentiation is integrated and converted as a input matrix for `Fisher.test` or `Stouffer.test`. Weight in each study can also be introduced.

### Usage

    other.oneside.pvalues(Upper, Lower, weight = NULL)

### Arguments

`Upper` | A matrix which means p-values or probability in one-sided test (positive differentiation). Its rows mean "gene" and its columns mean "study" that test was conducted.
`Lower` | A matrix which means p-values or probability in one-sided test (negative differentiation). Its rows mean "gene" and its columns mean "study" that test was conducted.
`weight` | A vector which means weight in each study. Its length must be equal to the number of column in Upper and Lower.

### Author(s)

Koki Tsuyuzaki, Itoshi Nikaido

### Examples

    ## Assume these are one-sided p-value generated by non-NOISeq method (e.g., cufflinks)
    upper <- matrix(runif(300), ncol=3, nrow=100)
    lower <- 1 - upper
    rownames(upper) <- paste0("Gene", 1:100)
    rownames(lower) <- paste0("Gene", 1:100)
    weight <- c(3,6,8)

    # other.oneside.pvalues function return a matrix which can input Fisher.test or Stouffer.test
    result <- other.oneside.pvalues(upper, lower, weight)

    # Fisher's method (without weighting)
    F <- Fisher.test(result)
    str(F)

    # Stouffer's method (with weighting by sample-size)
    S <- Stouffer.test(result)
    str(S)

[Package metaSeq version 1.20.0 Index]