isomiRs

Lorena Pantano edited this page Jan 22, 2018 · 4 revisions

Note:All the below doc is updated and only are here for historical reason. Ignore this section. Go to the main README for the current working tool

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<-loadIso(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<-makeCounts(obj)