stackedContrib2: Stacked Contribution

In alexjgriffith/mulcal: To facilitate the analysis of multiple ChIP-Seq data sets

Description

Stacked Contribution

Usage

stackedContrib2(data, tags, catagories, swCat = catagories, repls = FALSE,
  colors = FALSE, inord = seq(length(unique(swCat))), steps = 40,
  n = 10, f = c(function(x) {     mean(x) + sqrt(var(x)) * n }, function(x)
  {     mean(x) - sqrt(var(x)) * n }), sum = FALSE)

Author(s)

Alexander Griffith [e-mail]

Source

https://github.com/alexjgriffith/mulcal

Examples

tags<-read.table("~/Dropbox/UTX-Alex/jan/combined_sorted.bed")[,4]
catagories<-unique(unlist(lapply(levels(tags),strsplit,"-")))
values<-loadHeightFile("~/Dropbox/UTX-Alex/jan/combined_heights.bed")
data<-values$data
info<-values$info
pcs<-as.matrix(mulcal::ascore(data,c(1:10)))


swCat<-c("normal","normal","abnormal","abnormal","abnormal","abnormal","abnormal","abnormal","meka","ecfc","stem","stem")
swCat<-c("Erythroid","K562","Jurkat","CEM","RPMI","Prima5(Brand)","Prima2","Prima5","Megakaryocite","ECFC","CD133","CD34")
names(swCat)<-c("eryt","k562","jurk","cem","rpmi","tall_p1","tall_p2","tall_p3","meka","ecfc","cd133","cd34")
tSwCat<-as.character(unlist(lapply(catagories,function(x) swCat[x])))
stackedContrib(data,pcs[,1],catagories,tSwCat)

alexjgriffith/mulcal documentation built on May 10, 2019, 8:53 a.m.