MC3_Methods: List of level 3 multiple-concentration normalization methods

In tcpl: ToxCast Data Analysis Pipeline

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, "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 corrected values (cval) for neutral control wells (wllt = n).

bval.apid.lowconc.med

Calculate the baseline value (bval) as the plate-wise median, by assay plate ID (apid), of the corrected values (cval) for test compound wells (wllt = t) with a concentration index (cndx) of 1 or 2.

bval.apid.twlls.med

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

bval.apid.nwllslowconc.med

Calculate the baseline value (bval) as the plate-wise median, by assay plate ID (apid), of the corrected values (cval) of test compound wells (wllt = t) with a concentration index (cndx) of 1 or 2 or neutral control wells (wllt = n).

bval.spid.lowconc.med

Calculate the baseline value (bval) as the sample-wise median, by sample ID (spid), of the corrected values (cval) of the three lowest concentration test compound wells (wllt = t and cndx = 1, 2, & 3).

bval.apid.nwllstcwllslowconc.med

Calculate the baseline value (bval) as the plate-wise median, by assay plate ID (apid), of the corrected values (cval) for neutral control wells (wllt = n) or wells with a concentration index (cndx) of 1 or 2 and well type of test compound (wllt = t) or gain-of-signal control in multiple concentrations (wllt = c).

bval.aeid.nwlls.med

Calculate the baseline value (bval) as the endpoint-wise median, by assay component endpoint ID (aeid), corrected value (cval) for neutral control wells (wllt = n).

pval Methods

pval.apid.pwlls.med

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

pval.apid.pmv.min

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

pval.apid.pmv.max

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

pval.apid.f.max

Calculate the positive control value (pval) as the plate-wise maximum, by assay plate ID (apid), of the medians of important reference wells (wllt = f) values by apid and concentration.

pval.apid.f.min

Calculate the positive control value (pval) as the plate-wise minimum, by assay plate ID (apid), of the medians of important reference wells (wllt = f) values by apid and concentration.

pval.apid.p.max

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

pval.apid.p.min

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

pval.apid.v.min

Calculate the positive control value (pval) as the plate-wise minimum, by assay plate ID (apid), of the medians of the corrected values (cval) for viability control wells (wllt = v) by apid and concentration.

pval.zero

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

pval.apid.owlls.med

Calculate the positive control value (pval) as the plate-wise median, by assay plate ID (apid), of the corrected values (cval) for single-concentration negative control wells (wllt = o).

pval.2bval

Calculate the positive control value (pval) as the plate-wise median, by assay plate ID (apid), of the corrected values (cval) for neutral control wells (wllt = n) multiplied by 2.

pval.maxp

Calculate the positive control value (pval) as the endpoint-wise maximum, by assay component ID (aeid), of the corrected values for single-concentration gain-of-signal wells (wllt = p).

pval.apid.bwlls.med

Calculate the positive control value (pval) as the plate-wise median, by assay plate ID (apid), of the corrected values (cval) for blank wells (wllt= b).

pval.twlls.99pct

Calculate positive control value (pval) as the 99th percentile of all corrected value (cvals) of the test compound wells (wllt = t).

pval.neg.100

Calculate positive control value (pval) as -100 for endpoints in the down direction; pval = -100.

resp Methods

resp.pc

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

resp.pc.pval.cor

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

resp.fc

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

resp.logfc

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

resp.log2

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

resp.mult25

Multiply the normalized response value (resp) by 25; 25*resp.

resp.scale.mad.log2fc

Scale the normalized response value (resp) by the ratio of log2(1.2) and 3 multiplied by the baseline median absolute deviation (bmad) of the unscaled normalized response values (resp); (\log_{2}{1.2})/3*bmad*resp.

resp.scale.quant.log2fc

Scale the normalized response value (resp). First, determine the maximum difference (md) by finding the maximum between the absolute difference of the 1st percentile minus the 50th percentile and the absolute difference of the 99th percentile minus the 50th percentile. Then multiply resp by log2(1.2) divided by 20 percent of md; (\log_{2}{1.2})/0.2*md*resp.

resp.multneg1

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

resp.shiftneg.3bmad

Shift all the normalized response values (resp) less than -3 multiplied by the baseline median absolute deviation (bmad) to 0; if resp < -3*bmad,~resp = 0.

resp.shiftneg.6bmad

Shift all the normalized response values (resp) less than -6 multiplied by the baseline median absolute deviation (bmad) to 0; if resp < -6*bmad,~resp = 0.

resp.shiftneg.10bmad

Shift all the normalized response values (resp) less than 10 multiplied by the baseline median absolute deviation (bmad) to 0; if resp < -10*bmad,~resp = 0.

resp.blineshift.3bmad.repi

Shift the normalized response value (resp) with a baseline correction, by replicate index (repi), with a window of 3 multiplied by the baseline median absolute deviation (bmad).

resp.blineshift.50.repi

Shift the normalized response value (resp) with a baseline correction, by replicate index (repi), with a window of 50.

resp.blineshift.3bmad.spid

Shift the normalized response value (resp) with a baseline correction, by sample ID (spid), with a window of 3 multiplied by the baseline median absolute deviation (bmad).

resp.blineshift.50.spid

Shift the normalized response value (resp) with a baseline correction, by sample ID (spid), with a window of 50.

none

Set the corrected response value (cval) as the normalized response value (resp); cval = resp. No additional mc3 methods needed for endpoint-specific normalization.

resp.zerocenter.fc

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

resp.incr.zerocenter.fc

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

resp.mult100

Multiply the normalized response value (resp) by 100; 100*resp.

Note

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

See Also

mc3, Method functions to query what methods get applied to each aeid

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