MC3_Methods: List of level 3 multiple-concentration normalization methods
In USEPA/CompTox-ToxCast-tcpl: ToxCast Data Analysis Pipeline
MC3_Methods R Documentation
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
USEPA/CompTox-ToxCast-tcpl documentation built on April 22, 2024, 12:37 p.m.
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| MC3_Methods | R Documentation |
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
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