CumulativeVarPlot: Plot of the Cumulative Variance due to the Principal Components
Description
The function plots the cumulative variance of the principal components.
Usage
CumulativeVarPlot(out, ug = "unguided", ...)
Arguments
out
object resulting from gPCA.batchdetect() call.
ug
"guided" or "unguided". Do you want the cumulative variance from guided or unguided PCA plotted.
...
any other plot calls.
Details
This function plots the cumulative variance of the principal components from guided or unguided PCA calculated as (for the unguided case)
$$Var_l=\frac{\sum_{i=1}^l \var(PC_u)_i}{\sum_{i=1}^n \var(PC_u)_i}$$
for the $l$th principal component ($l=1,\dots,n$).
References
Reese, S. E., Archer, K. J., Therneau, T. M., Atkinson, E. J., Vachon, C. M., de Andrade, M., Kocher, J. A., and Eckel-Passow, J. E. A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal components analysis. Bioinformatics, (in review).