SC1_Methods: List of level 1 single-concentration normalization functions

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

List of level 1 single-concentration normalization functions

Description

sc1_mthds returns a list of functions to be used during level 1 single-concentration processing.

Usage

sc1_mthds()

Details

The functions contained in the list returned by sc1_mthds return a list of expressions to be executed in the sc2 (not exported) function environment. The functions are described here for reference purposes, The sc1_mthds function is not exported, nor is it intended for use.

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

Value

A list 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 acid.

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

bval Methods

bval.apid.nwlls.med

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

bval.apid.twlls.med

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

bval.apid.tn.med

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

pval Methods

pval.apid.pwlls.med

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

pval.apid.mwlls.med

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

pval.apid.medpcbyconc.max

First calculate the median of rval 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 rval 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 rval 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.zero

Define pval as 0.

resp Methods

resp.pc

Calculate resp as \frac{\mathit{rval} - \mathit{bval}}{\mathit{pval} - \mathit{bval}}100.

resp.fc

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

resp.logfc

Calculate resp as \mathit{rval} - \mathit{bval}.

resp.log2

Take the logarithm of resp with base 2.

resp.multneg1

Multiply resp by -1.

none

Do no normalization; make resp equal to rval.

Note

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

See Also

sc1, Method functions to query what methods get applied to each acid

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