plotRP: Graphical Display of the Rank Product/Sum analysis

In RankProd: Rank Product method for identifying differentially expressed genes with application in meta-analysis

Description

Plot a graph of the estimated pfp vs the number of identified genes

Usage

plotRP(x, cutoff=NULL)

Arguments

x	the value returned by function RP, RPadvance, RSadvance, RankProducts or RP.advance
cutoff	The pfp threshold value used to select genes

Value

A graphical display of the estimated pfp vs number of identified genes, which is also the gene rank of its original rank product/sum across all comparison. If cutoff is sepcified, a horizontal line will be plotted on the graphic to indicate the positon of the cutoff point, and all genes identified will be marked in red.

Two plots will be displayed, one for the identification of up-regulated genes in class 2, one for the identification of down-regulated genes in class 2

Author(s)

Fangxin Hong, [e-mail]
Francesco Del Carratore, [e-mail]

See Also

topGene RP RPadvance RSadvance

Examples

# Load the data of Golub et al. (1999). data(golub) 
#contains a 3051x38 gene expression
# matrix called golub, a vector of length called golub.cl 
#that consists of the 38 class labels,
# and a matrix called golub.gnames whose third column contains the gene names.
data(golub)
 
#use a subset of data as example, apply the rank product method
subset <- c(1:4,28:30)
#Setting rand=123, to make the results reproducible,
#identify genes that are up-regulated in class 2 
#(class label =1)
RP.out <- RP(golub[,subset],golub.cl[subset], rand=123)
      
#plot the results
plotRP(RP.out,cutoff=0.05)

Example output

Loading required package: Rmpfr
Loading required package: gmp

Attaching package: ‘gmp’

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

    %*%, apply, crossprod, matrix, tcrossprod

C code of R package 'Rmpfr': GMP using 64 bits per limb


Attaching package: ‘Rmpfr’

The following object is masked from ‘package:gmp’:

    outer

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

    dbinom, dgamma, dnbinom, dnorm, dpois, pnorm

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

    cbind, pmax, pmin, rbind

Rank Product analysis for unpaired case 
 

 done  

RankProd documentation built on Nov. 8, 2020, 8 p.m.