gRxCluster: gRxCluster

In geneRxCluster: gRx Differential Clustering

Description

cluster integration sites - optionally perform the permutations needed to estimate the discoveries expected under a null hypothesis

Usage

gRxCluster(object, starts, group, kvals, nperm = 0L,
  pruneFun = prune.loglik, ..., cutpt.filter.expr, cutpt.tail.expr, tmp.env,
  sample.id, sample.tab)

Arguments

object	chromosome names or other grouping of starts
starts	ordered chromosome position or ordered integer vector
group	logical vector separating two groups
kvals	integer vector of window widths
nperm	number of permutations for FDR calculation
pruneFun	a function like prune.loglik.
...	other args
cutpt.filter.expr	(optional) R object or call (or variable naming a call) with (optional) var x (window widths in base pairs) to filter windows. It must evaluate to mode "double". If not specified, as.double(apply(x,2,median,na.rm=TRUE)) is used. If an atomic vector of length one is supplied it is expanded to the proper length and coerced to double. If this arg is the name of a variable provided in tmp.env, it must be protected with quote(...).
cutpt.tail.expr	R object or call (or variable naming a call) with (optional) vars: k,n, and x (as above). Returns list like critVal.target. k is a vector of the number of sites in a collection of windows, and n is a vector of counts or proportions for the two classes of insertion. If not supplied, critVal.target(k,n,target=5,posdiff=x) is used. If this arg is the name of a variable provided in tmp.env, it must be protected with quote(...).
tmp.env	(optional) environment to use in evaluation of cutpt.* expressions. This is usually needed for critVal.power, which is first calculated and placed in the environment, and the supplied object is used in the expression for cutpt.filter.expr.
sample.id	(optional) integer vector indexing cells in sample.tab to be looked up to determine group under permutation. A factor can be used, too, but will be coerced to integer.
sample.tab	(optional) integer vector containing 0 or 1 in each cell. Its length is the same as max(sample.id). Both or neither sample.id and sample.tab should be supplied. When supplied sample.tab[sample.id] must equal group. If the arguments are supplied, permutations are of the form sample(sample.tab)[sample.id]. Otherwise they are of the form sample(group).

Value

a GRanges object with a special metadata slot, see gRxCluster-object

Author(s)

Charles Berry example inst/ex-gRxCluster.R

geneRxCluster documentation built on Nov. 8, 2020, 4:56 p.m.