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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/denoise.R
\name{smooth_via_pca}
\alias{smooth_via_pca}
\title{Smooth data by PCA}
\usage{
smooth_via_pca(
x,
elbow_th = 0.025,
dims_use = NULL,
max_pc = 100,
do_plot = FALSE,
scale. = FALSE
)
}
\arguments{
\item{x}{A data matrix with genes as rows and cells as columns}
\item{elbow_th}{The fraction of PC sdev drop that is considered significant; low values will lead to more PCs being used}
\item{dims_use}{Directly specify PCs to use, e.g. 1:10}
\item{max_pc}{Maximum number of PCs computed}
\item{do_plot}{Plot PC sdev and sdev drop}
\item{scale.}{Boolean indicating whether genes should be divided by standard deviation after centering and prior to PCA}
}
\value{
Smoothed data
}
\description{
Perform PCA, identify significant dimensions, and reverse the rotation using only significant dimensions.
}
\examples{
\donttest{
vst_out <- vst(pbmc)
y_smooth <- smooth_via_pca(vst_out$y, do_plot = TRUE)
}
}
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