plotGeneScore: Plot gene (DE/DS) scores

In SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Description

This function is to plot gene scores, as well as DE scores and DS scores

Usage

plotGeneScore(score, perm.score = NULL, pdf = NULL, 
              main = c("Overall", "Expression", "Splicing"))

Arguments

score	the gene/DE/DS score vector.
perm.score	a matrix of the corresponding gene/DE/DS scores on the permutation data sets.
pdf	if a PDF file name provided, plot will be save to that file.
main	the key words representing the type of scores that will be shown in the plot main title.

Details

The plot shows the ranked scores from the largest to the smallest. Lines also show the maximum and average scores, values shown on the top left.

Author(s)

Xi Wang, [e-mail]

Examples

data(DEscore, package="SeqGSEA")
plotGeneScore(DEscore, main="Expression")
data(DSscore, package="SeqGSEA")
gene.score <- geneScore(DEscore, DSscore, method="linear", DEweight = 0.3)
plotGeneScore(gene.score)

Example output

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: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: DESeq
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.

SeqGSEA documentation built on Nov. 8, 2020, 5:46 p.m.