MC3_Methods: List of level 3 multiple-concentration normalization methods

In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data

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 \frac{\mathit{cval} - \mathit{bval}}{\mathit{pval} - \mathit{bval}}100.

resp.fc

Calculate resp as \mathit{cval}/\mathit{bval}.

resp.logfc

Calculate resp as \mathit{cval} - \mathit{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 \frac{\log_2 \left( 1.2 \right)}{3\mathit{bmad}}.

resp.scale.quant.log2fc

Determine the maximum response \mathit{md} where \mathit{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 \log_2 \left( 1.2 \right).

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

pmpsa-hpc/GladiaTOX documentation built on Sept. 1, 2023, 5:52 p.m.