pvals: P-values or probability calculated by DESeq, edgeR, baySeq,...

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

Description

P-values or probability calculated by DESeq, edgeR, baySeq, NOISeq, and DEGSeq against StudyA, which was down-sampled simulation data (1, 1/2, 1/4, 1/8, 1/16, and 1/32).

Usage

data(pvals)

Source

https://trace.ddbj.nig.ac.jp/DRASearch/study?acc=SRP008746

See Also

StudyA, BreastCancer.

Examples

data(pvals)
names(pvals)

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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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
 [1] "DESeq"                 "edgeR"                 "baySeq"               
 [4] "NOISeq"                "DEGseq(LRT) + median"  "DEGseq(LRT) + loess"  
 [7] "DEGseq(FET) + median"  "DEGseq(FET) + loess"   "DEGseq(MARS) + median"
[10] "DEGseq(MARS) + loess" 

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