getBootCI {HeritSeq} | R Documentation |
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 |
Strains |
A |
which.features |
A |
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 |
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 \times
num.boot matrix of all bootsrapped VPC values.