other.oneside.pvalues {metaSeq} | R Documentation |
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.
other.oneside.pvalues(Upper, Lower, weight = NULL)
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. |
Koki Tsuyuzaki, Itoshi Nikaido
## 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)