MC5_Methods: Load list of level 5 multiple-concentration cutoff methods
In tcpl: ToxCast Data Analysis Pipeline
MC5_Methods R Documentation
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.
- fc0.3
Add a cutoff value of 0.3. 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.
- 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.
- 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.
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. 7, 2023, 1:06 a.m.
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| MC5_Methods | R Documentation |
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.
- fc0.3
Add a cutoff value of 0.3. 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.
- 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.
- 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.
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.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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