Description Usage Arguments Value Author(s) See Also Examples
Plot a graph of the estimated pfp vs the number of identified genes
the value returned by function RP, RPadvance, RSadvance, RankProducts or RP.advance
The pfp threshold value used to select genes
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
Fangxin Hong, email@example.com
Francesco Del Carratore, firstname.lastname@example.org
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# 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)
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
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