ProcessReplicate: ProcessReplicate: Core NNLS Regression for Individual...
In FracFixR: Compositional Statistical Framework for RNA Fractionation Analysis
ProcessReplicate R Documentation
ProcessReplicate: Core NNLS Regression for Individual Replicates
Description
This function implements the mathematical core of FracFixR: fitting a
non-negative least squares (NNLS) regression to estimate fraction weights
and correct individual transcript abundances.
Usage
ProcessReplicate(RepMat, transcriptlist)
Arguments
RepMat
Data frame with transcripts as rows, samples as columns.
Must include a "Total" column representing the whole cell lysate
transcriptlist
Character vector of transcript IDs to use for regression.
These should be informative transcripts in the appropriate abundance range
Details
Mathematical basis:
Total = \alpha_0 + \alpha_1 \times Fraction1 + \alpha_2 \times Fraction2 + ... + \epsilon
Where \alpha_0 represents the "lost" fraction and other \alpha_i are fraction weights
Value
List containing:
Propestimates: Proportion estimates for each transcript (values 0-1 for fraction columns)
NewData: Corrected count matrix (proportions multiplied by predicted total, rounded)
Coefficients: NNLS regression coefficients (fraction weights)
Fractions: Normalized fraction proportions
plot: Diagnostic plot of fitted vs residuals
FracFixR documentation built on May 11, 2026, 9:09 a.m.
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| ProcessReplicate | R Documentation |
ProcessReplicate: Core NNLS Regression for Individual Replicates
Description
This function implements the mathematical core of FracFixR: fitting a non-negative least squares (NNLS) regression to estimate fraction weights and correct individual transcript abundances.
Usage
ProcessReplicate(RepMat, transcriptlist)
Arguments
RepMat |
Data frame with transcripts as rows, samples as columns. Must include a "Total" column representing the whole cell lysate |
transcriptlist |
Character vector of transcript IDs to use for regression. These should be informative transcripts in the appropriate abundance range |
Details
Mathematical basis:
Total = \alpha_0 + \alpha_1 \times Fraction1 + \alpha_2 \times Fraction2 + ... + \epsilon
Where \alpha_0 represents the "lost" fraction and other \alpha_i are fraction weights
Value
List containing:
Propestimates: Proportion estimates for each transcript (values 0-1 for fraction columns)
NewData: Corrected count matrix (proportions multiplied by predicted total, rounded)
Coefficients: NNLS regression coefficients (fraction weights)
Fractions: Normalized fraction proportions
plot: Diagnostic plot of fitted vs residuals
R Package Documentation
Browse R Packages
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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