IsoPval.nm {NMTox}

Calculate p-values based on permutation for both increasing and decreasing ordered alternatives

Description

This function calculates p-values based on permutation. The plots of the null distribution and the observed test statistic under increasing and decreasing ordered alternatives are also given.

Usage

IsoPval.nm(data.nm, dose, response, stat=c("E2", "Williams","Marcus",
  "M", "ModM"), niter, nano.cat=NULL)

Arguments

data.nm

Nanomaterial dataset

dose

Dose or concentration (with the same unit of measurement)

response

Response (a certain endpoint value)

stat

Test statistics ("E2" for the global likelihood test, "Williams" for Williams test, "Marcus" for Marcus test, "M" for M test or "ModM" for modified M test)

niter

Number of permutations

nano.cat

Name of the nanomaterial

Details

This function is intended to be used inside the function Isotest. However, it can also be used to calculate p-values and generate the plot for one nanomaterial, with a particular unit of measurement of the dose, for a certain toxicity endpoint.

Value

This value provides p-values based on the permutation, the plot of the null distribution and the observed test statistics.

References

Lin D., Pramana, S., Verbeke, T., and Shkedy, Z. (2015). IsoGene: Order-Restricted Inference for Microarray Experiments. R package version 1.0-24. https://CRAN.R-project.org/package=IsoGene

Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens, L. (editors). (2012) Modeling Doseresponse Microarray Data in Early Drug Development Experiments Using R. Springer.

See Also

Isotest

Examples

#nm400 contains the result of genetic toxicity in vitro study of NM-400
#(Multi-walled carbon nanotubes) with associated controls
IsoPval.nm(data.nm=nm400, dose="concentration", response="value",
           stat="E2", niter=1000)