findVariableFeatures: Find highly variable peptides
In DavisLaboratory/msImpute: Imputation of label-free mass spectrometry peptides
View source: R/findVariableFeatures.R
findVariableFeatures R Documentation
Find highly variable peptides
Description
For each peptide, the total variance is decomposed into biological and technical variance using package scran
Usage
findVariableFeatures(y)
Arguments
y
numeric matrix giving log-intensity. Can contain NA values. Peptides with insufficient observations will be ignored.
Details
A loess trend is fitted to total sample variances and mean intensities. For each peptide, the biological variance is then
computed by subtracting the estimated technical variance from the loess fit from the total sample variance.
Value
A data frame where rows are peptides and columns contain estimates of biological and technical variances. Peptides are ordered by biological variance.
See Also
computeStructuralMetrics
Examples
data(pxd007959)
findVariableFeatures(data.matrix(log2(pxd007959$y)))
DavisLaboratory/msImpute documentation built on Jan. 5, 2024, 3:50 a.m.
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View source: R/findVariableFeatures.R
| findVariableFeatures | R Documentation |
Find highly variable peptides
Description
For each peptide, the total variance is decomposed into biological and technical variance using package scran
Usage
findVariableFeatures(y)
Arguments
y |
numeric matrix giving log-intensity. Can contain NA values. Peptides with insufficient observations will be ignored. |
Details
A loess trend is fitted to total sample variances and mean intensities. For each peptide, the biological variance is then computed by subtracting the estimated technical variance from the loess fit from the total sample variance.
Value
A data frame where rows are peptides and columns contain estimates of biological and technical variances. Peptides are ordered by biological variance.
See Also
computeStructuralMetrics
Examples
data(pxd007959)
findVariableFeatures(data.matrix(log2(pxd007959$y)))
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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