other.oneside.pvalues: Optional function for non-NOISeq method

In metaSeq: Meta-analysis of RNA-Seq count data in multiple studies

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)

Example output

Loading required package: NOISeq
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: splines
Loading required package: Matrix
Loading required package: snow

Attaching package: ‘snow’

The following objects are masked from ‘package:BiocGenerics’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, parApply, parCapply,
    parLapply, parRapply, parSapply

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
    parCapply, parLapply, parRapply, parSapply, splitIndices,
    stopCluster

Loading required package: Rcpp
List of 3
 $ Upper : Named num [1:100] 0.9748 0.00347 0.18337 0.4687 0.28737 ...
  ..- attr(*, "names")= chr [1:100] "Gene1" "Gene2" "Gene3" "Gene4" ...
 $ Lower : Named num [1:100] 0.0655 0.9992 0.889 0.461 0.6426 ...
  ..- attr(*, "names")= chr [1:100] "Gene1" "Gene2" "Gene3" "Gene4" ...
 $ Weight: Named num [1:3] 3 6 8
  ..- attr(*, "names")= chr [1:3] "Exp 1" "Exp 2" "Exp 3"
List of 3
 $ Upper : Named num [1:100] 0.93019 0.00409 0.24103 0.34207 0.29961 ...
  ..- attr(*, "names")= chr [1:100] "Gene1" "Gene2" "Gene3" "Gene4" ...
 $ Lower : Named num [1:100] 0.0698 0.9959 0.759 0.6579 0.7004 ...
  ..- attr(*, "names")= chr [1:100] "Gene1" "Gene2" "Gene3" "Gene4" ...
 $ Weight: Named num [1:3] 3 6 8
  ..- attr(*, "names")= chr [1:3] "Exp 1" "Exp 2" "Exp 3"

metaSeq documentation built on Nov. 8, 2020, 7:26 p.m.