isomiRs
Lorena edited this page Feb 26, 2014
·
4 revisions
Installation
library(devtools)
library(roxygen2)
devtools:install_local("$PATH2SEQBUSTER/R/isomiR_package/isomiRs")
library(isomiRs)
There is a R scripts and set of example data at folder $PATH2SEQBUSTER/R/isomiR_package/test
Load project
setwd("$PATH2SEQBUSTER/R/isomiR_package/test")
#files coming from miraligner(need to be run with flag -freq)
files<-c("y0d2.hsa.fa.ad.new.mirna",
"y0d34.hsa.fa.ad.new.mirna",
"y66d0.hsa.fa.ad.new.mirna",
"y80d0.hsa.fa.ad.new.mirna"
)
#data.matrix showing the design of the project.
#columns for the conditions
d<-data.frame(condition=c("p","p","c","c"))
#row.names for the sample names (I faked here)
row.names(d)<-paste(d[,1],1:2,sep="")
#create isomiR S4 object
obj<-loadIso2(files,d,skip=0,header=T)
plot isomiRs distributions among samples
obj<-plotIso(obj,type="sub")
Differential expression analysis. In this example I defined ref=T that means separate reference miRNA and isomiRs
#check diff exp: this will become a DESeq2 obj,
#so any function can be apply to this
dds<-deIso(obj,formula=~condition,ref=T)
#plotMA
library(DESeq2)
plotMA(dds)
access count data from dss object
table<-counts(dss)