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# SUBSET DATA SETS
assign("[.DGEList",
function(object, i, j, keep.lib.sizes=TRUE)
# Subsetting for DGEList objects
# 24 September 2009. Last modified 8 Feb 2015.
{
if(nargs() < 3) stop("Two subscripts required",call.=FALSE)
# Recognized components
IJ <- c("counts","pseudo.counts","offset","weights")
IX <- c("genes")
JX <- c("samples")
I <- c("AveLogCPM","trended.dispersion","tagwise.dispersion","prior.n","prior.df")
# Obsolete <- c("conc","infos","all.zeros")
out <- subsetListOfArrays(object,i,j,IJ=IJ,IX=IX,I=I,JX=JX)
if(!(missing(i) || keep.lib.sizes)) out$samples$lib.size <- colSums(out$counts)
if(!missing(j)) out$samples$group <- dropEmptyLevels(out$samples$group)
out
})
assign("[.DGEGLM",
function(object, i, j)
# Subsetting for DGEGLM objects
# 11 May 2011. Last modified 20 April 2016.
{
if(nargs() != 3) stop("Two subscripts required",call.=FALSE)
if(!missing(j)) stop("Subsetting columns not allowed for DGEGLM object.",call.=FALSE)
# Recognized components
IJ <- character(0)
IX <- c("counts","offset","weights","genes","coefficients","fitted.values","unshrunk.coefficients")
I <- c("AveLogCPM","dispersion","prior.n","prior.df","var.post","var.prior","df.prior","df.residual","df.residual.zeros","deviance","iter","failed")
JX <- character(0)
subsetListOfArrays(object,i,j,IJ=IJ,IX=IX,I=I,JX=JX)
})
assign("[.DGEExact",
function(object, i, j)
# Subsetting for DGEExact objects
# Davis McCarthy, Gordon Smyth
# 6 October 2010. Last modified 11 Dec 2013.
{
if(nargs() != 3) stop("Two subscripts required",call.=FALSE)
if(!missing(j)) stop("Subsetting columns not allowed for DGEExact objects.",call.=FALSE)
if(!missing(i)) {
object$table <- object$table[i,,drop=FALSE]
object$genes <- object$genes[i,,drop=FALSE]
}
object
})
assign("[.DGELRT",
function(object, i, j)
# Subsetting for DGELRT objects
# 6 April 2011. Last modified 20 April 2016.
{
if(nargs() != 3) stop("Two subscripts required",call.=FALSE)
if(!missing(j)) stop("Subsetting columns not allowed for DGELRT object.",call.=FALSE)
# Recognized components
IJ <- character(0)
IX <- c("counts","offset","weights","genes","coefficients","fitted.values","table","unshrunk.coefficients")
I <- c("AveLogCPM","dispersion","prior.n","prior.df","var.post","var.prior","df.prior","df.residual","df.residual.zeros","deviance","iter","failed","df.test","df.total")
JX <- character(0)
subsetListOfArrays(object,i,j,IJ=IJ,IX=IX,I=I,JX=JX)
})
assign("[.TopTags",
function(object, i, j)
# Subsetting for TopTags objects
# 7 October 2009. Last modified 11 Dec 2013.
{
if(nargs() != 3) stop("Two subscripts required",call.=FALSE)
if(!missing(i) || !missing(j)) object$table <- object$table[i,j,drop=FALSE]
object
})
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