getBootCI {HeritSeq}

Compute variance partition coefficition (VPC) confidence intervals (CI) for one or more features.

Description

Compute VPC CI based on parametric bootstrap for one or more features.

Usage

getBootCI(
  CountMatrix,
  Strains,
  which.features,
  num.boot,
  method = "NB-fit",
  alpha = 0.05,
  optimizer = "nlminb"
)

Arguments

CountMatrix

A G\times N count matrix. G is the number of features; N is the total number of samples.

Strains

A 1\times N vector of strain labels corresponding to each sample.

which.features

A 1\times k vector of select feature numbers for which CI is desired. k\leq G.

num.boot

Number of bootstraps.

method

Which method should be used, "CP-fit", "NB-fit" (default), or "VST". "VST" method bootstraps data under negative binomial mixed models.

alpha

A numerical value between 0 and 1, indicating the significance level of the CI. The CI will be 100*(1-\alpha) percent CI. Default value is 0.05.

optimizer

A character string that determines which optimization routine is to be used. It is only used for method = "CP-fit". Possible choices are "nlminb" (default), "L-BFGS-B", and "bobyqa".

Value

A list of two objects. The first object is a k \times 2 matrix containing the CI. The second object consists of a k \timesnum.boot matrix of all bootsrapped VPC values.