MC5_Methods: Load list of level 5 multiple-concentration cutoff methods

In tcpl: ToxCast Data Analysis Pipeline

Load list of level 5 multiple-concentration cutoff methods

Description

mc5_mthds returns a list of additional activity cutoff methods to be used during level 5 multiple-concentration processing.

Usage

mc5_mthds(ae)

Arguments

ae	Integer of length 1, the assay endpoint id

Details

The functions contained in the list returned by mc5_mthds take aeids (a numeric vector of aeid values) and returns a list of expressions to be executed in the mc5 (not exported) function environment. The functions are described here for reference purposes, The mc5_mthds function is not exported, nor is it intended for use.

All available methods are described in the "Available Methods" section, listed by the cutoff type in ascending order of cutoff value.

Value

A list of functions

Available Methods

The methods are broken down into five categories based on the type of cutoff they assign. Different methods are used to define cutoffs for "bmad" (baseline median absolute value), "fc" (fold change), "log" (\log_{2} or \log_{10}), "pc" (percent of control), and "other" (uncategorized cutoffs).

All methods are applied by aeid.

Although there are method exceptions (notably within the “other” category), only highest calculated cutoff value based on assigned methods will be selected for hitcalling. Therefore, only the largest cutoff method per method type should be assigned.

More information about the level 5 multiple-concentration processing is available in the package vignette, "Data_processing."

BMAD Methods

bmad1

Add a cutoff value of 1 multiplied by baseline median absolute value (bmad). By default, bmad is calculated using test compound wells (wllt = t) for the endpoint.

bmad2

Add a cutoff value of 2 multiplied by the baseline median absolute deviation (bmad). By default, bmad is calculated using test compound wells (wllt = t) for the endpoint.

bmad3

Add a cutoff value of 3 multiplied by the baseline median absolute deviation (bmad) as defined at Level 4.

bmad4

Add a cutoff value of 4 multiplied the baseline median absolute deviation (bmad). By default, bmad is calculated using test compound wells (wllt = t) for the endpoint.

bmad5

Add a cutoff value of 5 multiplied the baseline median absolute deviation (bmad). By default, bmad is calculated using test compound wells (wllt = t) for the endpoint.

bmad6

Add a cutoff value of 6 multiplied by the baseline median absolute deviation (bmad). By default, bmad is calculated using test compound wells (wllt = t) for the endpoint.

bmad10

Add a cutoff value of 10 multiplied by the baseline median absolute deviation (bmad). By default, bmad is calculated using test compound wells (wllt = t) for the endpoint.

Fold Change Methods

fc0.2

Add a cutoff value of 0.2. Typically for zero centered fold change data.

fc0.25

Add a cutoff value of 0.25. Typically for zero centered fold change data.

fc0.3

Add a cutoff value of 0.3. Typically for zero centered fold change data.

fc0.5

Add a cutoff value of 0.5. Typically for zero centered fold change data.

Log Methods

Log Base 2

neglog2_0.88

Add a cutoff value of -\log_{2}{0.88}.

log2_1.2

Add a cutoff value of \log_{2}{1.2}. Typically for fold change data.

log2_2

Add a cutoff value \log_{2}{2}. Typically for fold change data.

Log Base 10

log10_1.2

Add a cutoff value of \log_{10}{1.2}. Typically for fold change data.

log10_2

Add a cutoff value of \log_{10}{2}. Typically for fold change data.

Percent of Control Methods

pc05

Add a cutoff value of 5. Typically for percent of control data.

pc10

Add a cutoff value of 10. Typically for percent of control data.

pc16

Add a cutoff value of 16. Typically for percent of control data.

pc20

Add a cutoff value of 20. Typically for percent of control data.

pc25

Add a cutoff value of 25. Typically for percent of control data.

pc30

Add a cutoff value of 30. Typically for percent of control data.

pc40

Add a cutoff value of 40. Typically for percent of control data.

pc50

Add a cutoff value of 50. Typically for percent of control data.

pc70

Add a cutoff value of 70. Typically for percent of control data.

pc95

Add a cutoff value of 95. Typically for percent of control data.

Other Methods

maxmed20pct

Add a cutoff value of 20 percent of the maximum of all endpoint maximal average response values (max_med).

coff_2.32

Add a cutoff value of 2.32.

loec.coff

Method not yet updated for tcpl implementation. Identify the lowest observed effective concentration (loec) compared to baseline.

ow_bidirectional_loss

Multiply winning model hitcall (hitc) by -1 for models fit in the positive analysis direction. Typically used for endpoints where only negative responses are biologically relevant.

ow_bidirectional_gain

Multiply winning model hitcall (hitc) by -1 for models fit in the negative analysis direction. Typically used for endpoints where only positive responses are biologically relevant.

osd_coff_bmr

Overwrite the osd value so that bmr equals cutoff.

Note

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

See Also

mc5, Method functions to query what methods get applied to each aeid.

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