MC2_Methods: List of level 2 multiple-concentration correction functions

In tcpl: ToxCast Data Analysis Pipeline

List of level 2 multiple-concentration correction functions

Description

mc2_mthds returns a list of correction/transformation functions to be used during level 2 multiple-concentration processing.

Usage

mc2_mthds()

Details

The functions contained in the list returned by mc2_mthds return a list of expressions to be executed in the mc2 (not exported) function environment. The functions are described here for reference purposes, The mc2_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

More information about the level 2 multiple-concentration processing is available in the package vignette, "Data_processing."

Correction Methods

log2

Transform the corrected response value (cval) to log-scale (base 2).

log10

Transform the corrected response value (cval) to log-scale (base 10).

rmneg

Exclude wells with negative corrected response values (cval) and downgrading their well quality (wllq); if cval<0, wllq=0.

rmzero

Exclude wells with corrected response values (cval) equal to zero and downgrading their well quality (wllq); if cval=0, wllq=0.

mult25

Multiply corrected response value (cval) by 25; 25*cval.

mult100

Multiply corrected response value (cval) by 100; 100*cval.

negshift

Shift corrected response values (cval) by subtracting the minimum cval and adding 1, such that the new minimum is 1; cval-min+1.

mult2.5

Multiply corrected response value (cval) by 2.5; 2.5*cval.

mult3

Multiply corrected response value (cval) by 3; 3*cval.

mult6

Multiply corrected response value (cval) by 6; 6*cval.

sub100

Center data around zero by subtracting the corrected response value (cval) from 100; 100-cval. Typically used if data was pre-normalized around 100 with responses decreasing to 0.

zscore.npwlls

Convert the corrected response value (cval) to an absolute Z-Score based on the neutral and positive control wells (wllts = n and p), by assay plate ID (apid); cval=|(cval-mean(cval~for~wllt~=~n~and~p)/sd(cval~for~wllt~=~n~and~p)|.

sub1

Center data around zero by subtracting the corrected response value (cval) from 1; 1-cval. Typically used if data was pre-normalized around 1 with responses decreasing to 0.

Aggregation Methods

agg.mean.rep.apid

Aggregate technical test replicates (wllt=t) by taking the plate-wise mean per sample id (spid), assay plate (apid), and concentration index (cndx).

agg.median.rep.apid

Aggregate technical test replicates (wllt=t) by taking the plate-wise median per sample id (spid), assay plate (apid), and concentration index (cndx).

agg.percent.rep.spid

Use for binary data. Aggregate technical replicates as percentage by taking the sum of hits relative to total replicates per sample id (spid) and concentration index (cndx); cval = (sum(rval)/.N)*100.

agg.percent.rep.spid.min1

Use for binary data. Aggregate technical replicates as percentage by taking the sum of hits relative to total replicates per per sample id (spid) and concentration index (cndx), where there is more than one replicate; cval = (sum(rval)/.N)*100, where .N>1.

agg.mean.rep.apid

Aggregate technical replicates by taking the plate-wise mean per sample id (spid), assay plate (apid), and concentration index (cndx).

agg.median.rep.apid

Aggregate technical replicates by taking the plate-wise median per sample id (spid), assay plate (apid), and concentration index (cndx).

agg.percent.rep.spid

Use for binary data. Aggregate technical replicates as percentage by taking the sum of hits relative to total replicates per sample id (spid) and concentration index (cndx); cval = (sum(rval)/.N)*100.

agg.percent.rep.spid.min1

Use for binary data. Aggregate technical replicates as percentage by taking the sum of hits relative to total replicates per per sample id (spid) and concentration index (cndx), where there is more than one replicate; cval=(sum(rval)/.N)*100,~where~.N>1.

Note

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

See Also

mc2, Method functions to query what methods get applied to each acid

tcpl documentation built on Oct. 7, 2023, 1:06 a.m.