MC2_Methods {tcpl} | R Documentation |
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