SC2_Methods: List of level 2 single-concentration hit-call functions

In tcpl: ToxCast Data Analysis Pipeline

List of level 2 single-concentration hit-call functions

Description

sc2_mthds returns a list of functions to be used during level 2 single-concentration processing.

Usage

sc2_mthds()

Details

The functions contained in the list returned by sc2_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 sc2_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 down into four categories based on the type of cutoff they assign. Different methods are used to define cutoffs for "bmad" (baseline median absolute value), "pc" (percent of control), "pc or bmad", "log" (\log_{2} or \log_{10}), and "other" (uncategorized methods).

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 2 single-concentration processing is available in the package vignette, "Data_processing."

BMAD Methods

bmad1

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

bmad1.5

Add a cutoff value of 1.5 multiplied by the baseline median absolute deviation (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). 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.

Percent of Control Methods

pc0.88

Add a cutoff value of 0.88. 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.

Percent of Control or BMAD Methods

pc30orbmad3

Add a cutoff value of either 30 or 3 multiplied by the baseline median absolute deviation (bmad), whichever is less. By default, bmad is calculated using test compound wells (wllt = t) for the endpoint.

Log Methods

Log Base 2

log2_0.76

Add a cutoff value of 0.76 for log2-transformed data. This was a custom threshold value set for endpoint id 1690 (formerly aeid 1691).

log2_1.2

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

log2_1.5

Add a cutoff value of log_{2}{1.5}. 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.

Other Methods

ow_bmad_nwells

Overwrite the default baseline median absolute value (bmad) with a bmad calculated using neutral control wells (wllt = n).

ow_bidirectional_gain

Where responses only in the positive direction are biologically relevant, overwrite the max_med and max_tmp values, which were calculated using absolute value, to a calculation using a true maximum for uni-directional data.

ow_bidirectional_loss

Where responses only in the negative direction are biologically relevant, overwrite the max_med and max_tmp values, which were calculated using absolute value, to a calculation using a true minimum for uni-directional data.

Note

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

See Also

sc2, Method functions to query what methods get applied to each acid

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