thinCounts: Binomial or Multinomial Thinning of Counts

In edgeR: Empirical Analysis of Digital Gene Expression Data in R

Description

Reduce the size of Poisson-like counts by binomial thinning.

Usage

thinCounts(x, prob=NULL, target.size=min(colSums(x)))

Arguments

x	numeric vector or array of non-negative integers.
prob	numeric scalar or vector of same length as x, the expected proportion of the events to keep.
target.size	integer scale or vector of the same length as NCOL{x}, the desired total column counts. Must be not greater than column sum of x. Ignored if prob is not NULL.

Details

If prob is not NULL, then this function calls rbinom with size=x and prob=prob to generate the new counts. This is classic binomial thinning. The new column sums are random, with expected values determined by prob.

If prob is NULL, then this function does multinomial thinning of the counts to achieve specified column totals. The default behavior is to thin the columns to have the same column sum, equal to the smallest column sum of x.

If the elements of x are Poisson, then binomial thinning produces new Poisson random variables with expected values reduced by factor prob. If the elements of each column of x are multinomial, then multinomial thinning produces a new multinomial observation with a reduced sum.

Value

A vector or array of the same dimensions as x, with thinned counts.

Author(s)

Gordon Smyth

Examples

x <- rpois(10,lambda=10)
thinCounts(x,prob=0.5)

Example output

Loading required package: limma
 [1] 3 6 5 1 6 3 3 3 5 7

edgeR documentation built on Jan. 16, 2021, 2:03 a.m.