The data consists of case-control pairs. The pair of counts per pair and gene are compared by testing if the proportion of cases is equal to the proportion of the sample using the sizes of library (binomTest). It is assumed given (constant) the total count per pair and gene. These p-values are aggregated using OWA for a given orness. The weights of the OWA are calculated using the probability function of a binomial distribution.

pairedCounts(x, y, orness = 0.5, test, method = c("dbinom", "fuller"),
  is.decreasing = FALSE)

Arguments

x

Matrix expression

y

Design matrix (nrow(y) == ncol(x)). First column y[,1] is the block and second column y[,2] is the element within the block with values 0 (control) and 1 (case)

orness

The orness for OWA aggregation

test

Function to calculate the statistics per pairs

method

Aggregation method

is.decreasing

The values to aggregated should decreasing ordered

Value

A list with the aggregated p-values: result["dbinom"] and result["fuller"]

See also