meta.oneside.noiseq: One-sided NOISeq for meta-analysis
In metaSeq: Meta-analysis of RNA-Seq count data in multiple studies

Description Usage Arguments Author(s) References See Also Examples

NOISeq customized for one-sided test in meta-analysis. Parallel computing is also available by snow package.

meta.oneside.noiseq(input, k = 0.5, norm = c("rpkm", "uqua", "tmm", "n"), replicates = c("technical", "biological", "no"), factor = NULL, conditions = NULL, pnr = 0.2, nss = 5, v = 0.02, lc = 1, studies = NULL, cl = NULL)

`input`	Object of eSet class coming from readData function or other R packages such as DESeq.
`k`	Counts equal to 0 are replaced by k. By default, k = 0.5.
`norm`	Normalization method. It can be one of "rpkm" (default), "uqua" (upper quartile), "tmm" (trimmed mean of M) or "n" (no normalization).
`replicates`	In this argument, the type of replicates to be used is defined. Technical, biological or none. By default, technical replicates option is chosen. Note that "no" is automatically chosen against the study which has no replicate.
`factor`	A string indicating the name of factor whose levels are the conditions to be compared.
`conditions`	A vector containing the two conditions to be compared by the differential expression algorithm (needed when the factor contains more than 2 different conditions).
`pnr`	Percentage of the total reads used to simulated each sample when no replicates are available. By default, pnr = 0.2.
`nss`	Number of samples to simulate for each condition (nss>= 2). By default, nss = 5.
`v`	Variability in the simulated sample total reads. By default, v = 0.02. Sample total reads is computed as a random value from a uniform distribution in the interval [(pnr-v)sum(counts), (pnr+v)sum(counts)]
`lc`	Length correction is done by dividing expression by length^lc. By default, lc = 1.
`studies`	A vector specifying which column in data are measured in common study. Its length must be equal to the number of column in data.
`cl`	cluster object in snow pacakge.

Koki Tsuyuzaki, Itoshi Nikaido

Tarazona, S. and Garcia-Alcalde, F. and Dopazo, J. and Ferrer, A. and Conesa, A. (2011) Differential expression in RNA-seq: A matter of depth. Genome Research, 21(12): 2213-2223

noiseq

data(BreastCancer)
library("snow")

# Experimental condition (1: BreastCancer, 0: Normal)
flag1 <- c(1,1,1,0,0, 1,0, 1,1,1,1,1,1,1,0, 1,1,0)

# Source of data
flag2 <- c("A","A","A","A","A", "B","B", "C","C","C","C","C","C","C","C", "D","D","D")

# readData function for meta-analysis
cds <- meta.readData(data = BreastCancer, factor = flag1, studies = flag2)

# oneside NOISeq for meta-analysis
# cl <- makeCluster(4, "SOCK")
# result <- meta.oneside.noiseq(cds, k = 0.5, norm = "tmm", replicates = "biological", factor = flag1, conditions = c(1, 0), studies = flag2, cl = cl)
# stopCluster(cl)

# Script above is very time-consumming step. Please use this pre-calculated result instead
data(Result.Meta)
result <- Result.Meta

# 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)

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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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 [1:23368] 0.384 0.532 0.533 NA 0.136 ...
  ..- attr(*, "names")= chr [1:23368] "1/2-SBSRNA4" "A1BG" "A1BG-AS1" "A1CF" ...
 $ Lower : Named num [1:23368] 0.842 0.608 0.405 NA 0.366 ...
  ..- attr(*, "names")= chr [1:23368] "1/2-SBSRNA4" "A1BG" "A1BG-AS1" "A1CF" ...
 $ Weight: Named int [1:4] 5 2 8 3
  ..- attr(*, "names")= chr [1:4] "Study 1" "Study 2" "Study 3" "Study 4"
List of 3
 $ Upper : Named num [1:23368] 0.371 0.266 0.271 NA 0.296 ...
  ..- attr(*, "names")= chr [1:23368] "1/2-SBSRNA4" "A1BG" "A1BG-AS1" "A1CF" ...
 $ Lower : Named num [1:23368] 0.629 0.734 0.729 NA 0.704 ...
  ..- attr(*, "names")= chr [1:23368] "1/2-SBSRNA4" "A1BG" "A1BG-AS1" "A1CF" ...
 $ Weight: Named int [1:4] 5 2 8 3
  ..- attr(*, "names")= chr [1:4] "Study 1" "Study 2" "Study 3" "Study 4"