Type: | Package |
Title: | Melt Curve Fitting and Melt Shift Analysis |
Version: | 1.6 |
Description: | Analyzes raw abundance data from a cellular thermal shift experiment and calculates melt temperatures and melt shifts for each protein in the experiment. McCracken (2022) <doi:10.1101/2022.12.30.522131>. |
License: | GPL-2 |
Encoding: | UTF-8 |
Imports: | readxl, data.table, plotrix, tidyr, ggplot2, xlsx, httr, jsonlite, GGally, network, stats, RColorBrewer, svglite |
Suggests: | knitr, rmarkdown, |
VignetteBuilder: | knitr |
RoxygenNote: | 7.2.3 |
NeedsCompilation: | no |
Packaged: | 2023-04-18 23:04:43 UTC; namccrac |
Config/testthat/edition: | 3 |
Author: | Neil McCracken [aut], Hao Liu [ctb], Amber Mosley [cre] |
Maintainer: | Amber Mosley <almosley@iu.edu> |
Repository: | CRAN |
Date/Publication: | 2023-04-19 08:00:03 UTC |
This function corrects the normalized abundance of each protein using a correction constant that is calculated in this function. The correction constant is determined using the difference between actual and predicted fit at the proteome level.
Description
This function corrects the normalized abundance of each protein using a correction constant that is calculated in this function. The correction constant is determined using the difference between actual and predicted fit at the proteome level.
Usage
Correction(PSM, UP, Data_CurveFit1Parameters, Data_Normalized, Data_Quantified)
Arguments
PSM |
the number of peptide spectrum matches that are deemed acceptable for reporting |
UP |
the number of unique peptides for a protein that are deemed acceptable for reporting |
Data_CurveFit1Parameters |
the parameters determined from Curve Fit 1 operation for proteome melts |
Data_Normalized |
the normalized abundance data for each protein determined in the Normalize function. |
Data_Quantified |
the median normalized abundance data at the proteome level |
Value
the corrected and normalized abundance data for each protein
Examples
## Not run:
Data_Corrected<-Correction(PSM,UP,Data_CurveFit1Parameters,
Data_Normalized,Data_Quantified)
## End(Not run)
This function determines the 4 parameter or 3 parameter log fit for the proteome level curve.
Description
This function determines the 4 parameter or 3 parameter log fit for the proteome level curve.
Usage
CurveFit1(Data_Quantified)
Arguments
Data_Quantified |
the median abundance values calculated in the Quantify function |
Value
the curve fit parameters for the control and condition curves at the proteome level
Examples
## Not run:
Data_CurveFit1Parameters<-CurveFit1(Data_Quantified)
## End(Not run)
This function determines the best curve fit for each protein using the data post correction and also determines the R squared for each curve fit
Description
This function determines the best curve fit for each protein using the data post correction and also determines the R squared for each curve fit
Usage
CurveFit2(Data_Corrected)
Arguments
Data_Corrected |
data that meets exclusion criteria from Exclude function |
Value
Curve fits and R squared for each protein
Examples
## Not run:
Data_CurveFit2_Control<-CurveFit2(Data_Corrected_Control)
## End(Not run)
This function imports data that will be analyzed in downstream functions.
Description
This function imports data that will be analyzed in downstream functions.
Usage
Import(NControl, NCondition, Directory)
Arguments
NControl |
the number of Control replicate experiments that are to be analyzed |
NCondition |
the number of Condition replicate experiments that are to be analyzed |
Directory |
the directory where the source data files to be analyzed are saved. This is also the location where the results will be saved. |
Value
Imported data from all experiments
Examples
## Not run:
Data_Imported<-Import(NControl,NCondition,Directory)
## End(Not run)
This function is the primary function that calls other functions in the program.
Description
This function is the primary function that calls other functions in the program.
Usage
InflectSSP(
Directory,
NControl,
NCondition,
PSM,
UP,
CurveRsq,
PValMelt,
PValMeltFDR,
MeltLimit,
RunSTRING,
STRINGScore,
Species
)
Arguments
Directory |
the directory where the source data files to be analyzed are saved. This is also the location where the results will be saved. |
NControl |
the number of Control replicate experiments that are to be analyzed |
NCondition |
the number of Condition replicate experiments that are to be analyzed |
PSM |
the number of peptide spectrum matches that are deemed acceptable for reporting |
UP |
the number of unique peptides for a protein that are deemed acceptable for reporting |
CurveRsq |
Coefficient of determination criteria for melt curves |
PValMelt |
p-value criteria for melt shifts |
PValMeltFDR |
Whether or not the FDR correction for pvalue is used in designation of melts of interest |
MeltLimit |
the melt shift temperature limit used for determining which proteins to report as significant |
RunSTRING |
whether or not the STRING function will be run or not in the analysis |
STRINGScore |
the score to be used in the STRING analysis |
Species |
species number for bioinformatics search |
Value
the proteins that have significant melt shifts from an experiment
Examples
## Not run:
Directory<-'/Users/Einstein'
NControl<-2
NCondition<-3
PSM<-2
UP<-3
CurveRsq<-.95
PValMelt<-0.05
PValMeltFDR<-"No"
MeltLimit<-3
RunSTRING<-"Yes"
STRINGScore<-0.99
Species<-9606
InflectSSP(Directory,NControl,
NCondition,PSM,UP,CurveRsq,PValMelt,PValMeltFDR,
MeltLimit,RunSTRING,STRINGScore,
Species)
## End(Not run)
This function determines melt shifts for all proteins that meet quality criteria and also determines the melt shift p-values
Description
This function determines melt shifts for all proteins that meet quality criteria and also determines the melt shift p-values
Usage
MeltCalc(
Directory,
Data_CurveFit2_Complete_Unique,
CurveRsq,
PValMelt,
MeltLimit,
PValMeltFDR
)
Arguments
Directory |
the directory data is saved to |
Data_CurveFit2_Complete_Unique |
the curve fit data from the CurveFit2 function |
CurveRsq |
the criteria for melt curve p-values |
PValMelt |
the criteria for the melt shift p-values |
MeltLimit |
the melt shift temperature limit used for determining which proteins are significant |
PValMeltFDR |
Whether or not the FDR correction for pvalue is used in designation of melts of interest |
Value
Proteins melt shifts
Examples
## Not run:
Data_Melts<-MeltCalc(Directory,Data_CurveFit2_Complete_Unique,
CurveRsq,PValMelt,MeltLimit,PValMeltFDR)
## End(Not run)
This function normalizes the abundance values to that measured at the lowest temperature
Description
This function normalizes the abundance values to that measured at the lowest temperature
Usage
Normalize(Data_Imported)
Arguments
Data_Imported |
the abundance data imported from Import function |
Value
Normalized data
Examples
## Not run:
Data_Normalized<-Normalize(Data_Imported)
## End(Not run)
This function determines the median abundance value across the proteome for all experiments together
Description
This function determines the median abundance value across the proteome for all experiments together
Usage
Quantify(Data_Normalized, NReps)
Arguments
Data_Normalized |
the normalized abundance data calculated in the Normalize function |
NReps |
the number of replicates to be analyzed |
Value
The median abundance data for all experiments at the proteome level
Examples
## Not run:
Data_Quantified<-Quantify(Data_Normalized)
## End(Not run)
This function generates results from the Inflect function after applying criteria input from the user
Description
This function generates results from the Inflect function after applying criteria input from the user
Usage
ReportDataMelts(
Data_Melts,
Data_CurveFit2_Control,
Data_CurveFit2_Condition,
Directory,
PValMelt
)
Arguments
Data_Melts |
abundance and fit data for proteins that meet quality criteria in overall workflow |
Data_CurveFit2_Control |
the curve fit data from the Curve Fit 2 function |
Data_CurveFit2_Condition |
the curve fit data from the Curve Fit 2 function |
Directory |
directory where data is saved |
PValMelt |
the criteria for the melt shift p-values |
Value
Excel files with summary of data along with melt curve plots for significant proteins
Examples
## Not run:
ReportDataMelts(Data_Melts,Data_CurveFit2_Control,Data_CurveFit2_Condition,Directory,PValMelt)
## End(Not run)
This function generates a STRING based network using the significant melt shifts from analysis
Description
This function generates a STRING based network using the significant melt shifts from analysis
Usage
ReportSTRING(Data_Melts, STRINGScore, Directory, Species, PValMeltFDR)
Arguments
Data_Melts |
abundance and fit data for proteins that meet quality criteria in overall workflow |
STRINGScore |
the STRING score that is used to determine whether an interaction is significant |
Directory |
directory where results are saved |
Species |
species taxon number for bioinformatics search |
PValMeltFDR |
Whether or not the FDR correction for pvalue is used in designation of melts of interest |
Value
Excel files with summary of data along with melt curve plots for significant proteins
Examples
## Not run:
ReportSTRING(Data_Melts,STRINGScore,Directory,Species,PValMeltFDR)
## End(Not run)