SC1_Methods {GladiaTOX} | R Documentation

## 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 (rval - bval)/(pval - bval)*100.

resp.fc

  Calculate resp as rval/bval.

resp.logfc

  Calculate resp as rval - 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

[Package GladiaTOX version 1.0.0 Index]