Collapse multiple technical replicate count columns into two columns for plotting

Description

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Usage

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collapseRepliCounts(x, pair=nv(levels(x$samples$group)[1:2] , c('ref','obs')))

Arguments

x

a MANTA object.

pair

the pairs indicating which columns to collapse

Value

a collapsed, two-column count table

See Also

DGEList, manta

Examples

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cts <- matrix(data=rnbinom(28,2,.4), ncol=4, nrow=7)

colnames(cts) <- apply(expand.grid(c('a','b'),1:2), 1, paste, collapse='_')

x <- manta(cts, makeSampleDF(cts, group=rep(c('a','b'),2)))
collapseRepliCounts(x, pair=c('a','b'))