SC1_Methods: 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()

Arguments

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.

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.