MC3_Methods {GladiaTOX} | R Documentation

## List of level 3 multiple-concentration normalization methods

### Description

`mc3_mthds` returns a list of normalization methods to be used during level 3 multiple-concentration processing.

### Usage

    mc3_mthds()

### Details

The functions contained in the list returned by `mc3_mthds` take 'aeids' (a numeric vector of aeid values) and returns a list of expressions to be executed in the `mc3` (not exported) function environment. The functions are described here for reference purposes, The `mc3_mthds` function is not exported, nor is it intended for use.

All available methods are described in the Available Methods section, listed by the type of function and the function/method name.

### Value

A list of functions

### Available Methods

The methods are broken into three types, based on what fields they define. Different methods are used to define "bval" (the baseline value), "pval" (the positive control value), and "resp" (the final response value).

Although it does not say so specifically in each description, all methods are applied by aeid.

More information about the level 3 multiple-concentration processing is available in the package vignette, "Pipeline_Overview."

#### bval Methods

bval.apid.nwlls.med

  Calculate bval as the median of cval for wells with wllt equal to "n," by apid.

bval.apid.1owconc.med

  Calculate bval as the median of cval for wells with wllt equal to "t" and cndx equal to 1 or 2, by apid.

bval.apid.twlls.med

  Calculate bval as the median of cval for wells with wllt equal to "t," by apid.

bval.apid.tn.med

  Calculate bval as the median of cval for wells with wllt equal to "t" or "n," by apid.

bval.apid.nwllslowconc.med

  Calculate bval as the median of cval for wells with wllt equal to "n" or wells with wllt equal to "t" and cndx equal to 1 or 2, by apid.

bval.spid.lowconc.med

  Calculate bval as the median of cval for wells with wllt equal to "t" and cndx equal to 1, 2, or 3, by spid.

#### pval Methods

pval.apid.pwlls.med

  Calculate pval as the median of cval for wells with wllt equal to "p," by apid.

pval.apid.mwlls.med

  Calculate pval as the median of cval for wells with wllt equal to "m," by apid.

pval.apid.medpcbyconc.max

  First calculate the median of cval for wells with wllt equal to "p" or "c," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.

pval.apid.medpcbyconc.min

  First calculate the median of cval for wells with wllt equal to "p" or "c," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

pval.apid.medncbyconc.min

  First calculate the median of cval for wells with wllt equal to "m" or "o," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

pval.apid.pmv.min

  First calculate the median of cval for wells with wllt equal to "p," "m," or "v," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

pval.apid.pmv.max

  First calculate the median of cval for wells with wllt equal to "p," "m," or "v," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.

pval.apid.f.max

  First calculate the median of cval for wells with wllt equal to "f," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.

pval.apid.f.min

  First calculate the median of cval for wells with wllt equal to "f," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

pval.apid.p.max

  First calculate the median of cval for wells with wllt equal to "p," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.

pval.apid.p.min

  First calculate the median of cval for wells with wllt equal to "p," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

pval.apid.v.min

  First calculate the median of cval for wells with wllt equal to "v," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

pval.zero

  Define pval as 0.

#### resp Methods

resp.pc

  Calculate resp as (cval - bval)/(pval - bval)*100.

resp.fc

  Calculate resp as cval/bval.

resp.logfc

  Calculate resp as cval - bval.

resp.log2

  Take the logarithm of resp with base 2.

resp.mult25

  Multiply resp by 25.

resp.scale.mad.log2fc

  Multiply resp by the scale factor log2(1.2)/(3*bmad).

resp.scale.quant.log2fc

  Determine the maximum response md where md = abs(1st centile - 50th centile) or abs(99th centile - 50th centile), whichever is greater. Scale the response such that 20 percent of md equals log2(1.2).

resp.multneg1

  Multiply resp by -1.

resp.shiftneg.3bmad

  Shift all resp values less than 3*bmad to 0.

resp.shiftneg.6bmad

  Shift all resp values less than 6*bmad to 0.

resp.shiftneg.10bmad

  Shift all resp values less than 10*bmad to 0.

resp.blineshift.3bmad.repi

  Shift resp values with the blineShift function by repi, where the window (wndw) is 3*bmad.

resp.blineshift.50.repi

  Shift resp values with the blineShift function by repi, where the window (wndw) is 50.

resp.blineshift.3bmad.spid

  Shift resp values with the blineShift function by spid, where the window (wndw) is 3*bmad.

resp.blineshift.50.spid

  Shift resp values with the blineShift function by spid, where the window (wndw) is 50.

none

  Do no normalization; make resp equal to cval.

### Note

This function is not exported and is not intended to be used by the user.

### See Also

`mc3`, `gtoxMthdLoad` to query what methods get applied to each aeid

[Package GladiaTOX version 1.8.0 Index]