SC1_Methods: List of level 1 single-concentration normalization functions

In tcpl: ToxCast Data Analysis Pipeline

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, "Data_processing."

bval Methods

bval.apid.nwlls.med

Calculate the baseline value (bval) as the plate-wise median, by assay plate ID (apid), of the raw values (rval) for neutral control wells (wllt = n).

bval.apid.twlls.med

Calculate the baseline value (bval) as the plate-wise median, by assay plate ID (apid), of the raw values (rval) for test compound wells (wllt = t).

bval.apid.tn.med

Calculate the baseline value (bval) as the plate-wise median, by assay plate ID (apid), of the raw values (rval) for test compound wells (wllt = t) and neutral control wells (wllt = n).

bval.nwlls.med

Calculate the baseline value (bval) as the median of the raw values (rval) for neutral control wells (wllt = n) by assay endpoint id (aeid).

pval Methods

pval.apid.pwlls.med

Calculate the positive control value (pval) as the plate-wise median, by assay plate ID (apid), of the raw values (rval) for single-concentration gain-of-signal positive control wells (wllt = p).

pval.apid.mwlls.med

Calculate the positive control value (pval) as the plate-wise median, by assay plate ID (apid), of the raw values (rval) for multiple-concentration loss-of-signal negative control wells (wllt = m).

pval.apid.medpcbyconc.max

Calculate the positive control value (pval) as the plate-wise maximum, by assay plate ID (apid), of the medians of the raw values (rval) for gain-of-signal single- or multiple-concentration positive control wells (wllt = p or c) by apid, well type, and concentration.

pval.apid.medpcbyconc.min

Calculate the positive control value (pval) as the plate-wise minimum, by assay plate ID (apid), of the medians of the raw values (rval) for gain-of-signal single- or multiple-concentration positive control wells (wllt = p or c) by apid, well type, and concentration.

pval.apid.medncbyconc.min

Calculate the positive control value (pval) as the plate-wise minimum, by assay plate ID (apid), of the medians of the raw values (rval) for gain-of-signal single- or multiple-concentration negative control wells (wllt = m or o) by apid, well type, and concentration.

pval.zero

Set the positive control value (pval) to 0; pval = 0.

pval.apid.or.aeid.pwlls.med

Calculate the positive control value (pval) as the plate-wise median, by assay plate ID (apid), of the raw values (rval) for single-concentration gain-of-signal positive control wells (wllt = p). For plates without p wells, set the pval as the median pval calculated from all plates.

resp Methods

resp.pc

Calculate the normalized response (resp) as a percent of control, i.e. the ratio of the difference between the raw (rval) and baseline (bval) values divided by the difference between positive control (pval) and baseline (bval) values multiplied by 100; resp=(rval-bval)/(pval-bval)*100.

resp.fc

Calculate the normalized response (resp) as fold change, i.e. the ratio of the raw (rval) and baseline (bval) values; resp = rval/bval.

resp.logfc

Calculate the normalized response (resp) as the fold change of logged, i.e. the difference between raw (rval) and baseline (bval) log-scale values.

resp.log2

Transform the response values to log-scale (base 2).

resp.multneg1

Multiply the normalized response value (resp) by -1; -1*resp.

none

Use raw value (rval) as is. This may be necessary for additional endpoint-specific adjustments, or where no additional sc1 methods are needed.

resp.incr.zerocenter.fc

Calculate the normalized response (resp) as a zero center fold change, i.e. the ratio of the raw (rval) and baseline (bval) values minus 1; resp=rval/bval-1. Typically used for increasing responses.

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

tcpl documentation built on Oct. 10, 2024, 1:07 a.m.