DESCEND.control: The control parameters of the function 'runDescend' and...

Description Usage Arguments

View source: R/deconvSingle.R

Description

The control parameters of the function runDescend and deconvSingle

Usage

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DESCEND.control(n.points = 50, nStart = 2, nStart.lrt = 2,
  max.sparse = c(0.99, 20), LRT.Z.select = T, LRT.Z0.select = T,
  LRT.Z.values = 0, zeroInflate = T, dense.add.0 = T, only.integer = F,
  rel.info.range = c(5e-04, 0.01), rel.info.guide = 0.005, c0.start = 1,
  aStart = 1, bStart = 0, gStart = 0, start.sd = 0.2, penalty.Z0 = T,
  pDegree = 5, max.c0.iter = 5, c0.min = 1e-05)

Arguments

n.points

number of discritized points of the underlying true expression distribution. Default is 50

nStart

number of random starts for the optimization problem (as it is non-convex) to find the global minimum. Default is 2

nStart.lrt

number of random starts for the unpenalized optimization problem for likelihood ratio testing

max.sparse

a vector of 2 indicating the maximum sparsity allowed for a gene to be computed. The first element is the fraction of zero-counts allowed, the second element is the minimum number of non-zero counts. Both criteria should be satisfied. Default is (0.99, 20). For studying nonzero fraction, one should increase the threshold to get estimates with acceptable accuracy.

LRT.Z.select

a vector of length 1 or the number of columns of Z indicating for which column of Z the coefficients are tested against the corresponding value in LRT.Z.values using LRT. Default is TRUE, meaning that all columns are tested when LRT tests are performed.

LRT.Z0.select

a vector of length 1 or the number of columns of Z0 indicating for which column of Z0 the coefficients are tested against 0 using LRT. Default is TRUE, meaning that all columns are tested when LRT tests are performed.

LRT.Z.values

a vector of length 1 or the number of columns of Z showing the values that LRT tests on coefficients of Z are tested against. Default value is 0, meanings that all tests are tested against 0.

zeroInflate

whether to include the zero inflation part to the deconvolved distribution. Default is TRUE

dense.add.0

whether smooth the density at 0 into density.points in the output DESCEND object

only.integer

whether set the discrete points to be integers. Default is FALSE

rel.info.range

the relative information range allowed for finding the optimal tuning parameter c0

rel.info.guide

one parameter inside the rel.info.range controling for the searching process of c0

c0.start

the starting value of c0. Default is 1

aStart

the starting values of the spline coefficients of the deconvolved distribution

bStart

the starting values of the coefficients of Z0

gStart

the starting values of the coefficients of Z

start.sd

standard deviation of the random starting values when nStart > 1

penalty.Z0

whether add penalty to the coefficients of Z0 or not in optimization. Default is TRUE

pDegree

degree of the spline bases. Default is 5

max.c0.iter

maximum iteration allowed to find the optimal c0

c0.min

minimum c0 allowed to avoid degeneration


jingshuw/descend documentation built on Sept. 2, 2018, 11:10 a.m.