# INFO: function for analysis of rnaseq data
# DATE: 20.05.2011.
# AUTH: v+
# ---------------------------------------- #
MakeBinaryContrasts = function(v){
v = unique(v)
estatus = expand.grid(Var1=v, Var2=v)
estatus = estatus[!duplicated(apply(estatus, 1, function(x)paste(sort(x), collapse=":"))),]
estatus = subset(estatus, Var1 != Var2)
estatus = Reduce(function(...)paste(..., sep='-'), estatus)
return(estatus)
}
# {{2}}
# does DESeq differential expression on a table of counts
# for no replicates
# DiffExpNoRep = function(expr){
#
# library(DESeq)
# cds = newCountDataSet(expr, c('T','N'))
# cds = estimateSizeFactors(cds)
# cds = estimateVarianceFunctions(cds, method="blind" )
# d = nbinomTest(cds, 'T', 'N')
# d$padj[is.na(d$padj)] = 1
# return(d)
# }
#
# one sample has replicates
# DiffExpOneRep = function(expr){
#
# library(DESeq)
# cds = newCountDataSet(expr, c('T','N'))
# cds = estimateSizeFactors(cds)
# cds = estimateVarianceFunctions(cds, method="blind" )
# d = nbinomTest(cds, 'T', 'N')
# d$padj[is.na(d$padj)] = 1
# return(d)
# }
#/{{2}}
#/{1} FUNCTIONS
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