RunPCA.PSI: Principle component analysis for splicing data

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

Principle component analysis for splicing data

Description

Performs principle component analysis using PSI values.

Usage

RunPCA.PSI(
  MarvelObject,
  sample.ids = NULL,
  cell.group.column,
  cell.group.order,
  cell.group.colors = NULL,
  features,
  min.cells = 25,
  point.size = 0.5,
  point.alpha = 0.75,
  point.stroke = 0.1,
  seed = 1,
  method.impute = "random",
  cell.group.column.impute = NULL
)

Arguments

MarvelObject	Marvel object. S3 object generated from TransformExpValues function.
sample.ids	Character strings. Specific cells to plot.
cell.group.column	Character string. The name of the sample metadata column in which the variables will be used to label the cell groups on the PCA.
cell.group.order	Character string. The order of the variables under the sample metadata column specified in cell.group.column to appear in the PCA cell group legend.
cell.group.colors	Character string. Vector of colors for the cell groups specified for PCA analysis using cell.type.columns and cell.group.order. If not specified, default ggplot2 colors will be used.
features	Character string. Vector of tran_id for analysis. Should match tran_id column of MarvelObject$ValidatedSpliceFeature.
min.cells	Numeric value. The minimum no. of cells expressing the splicing event to be included for analysis.
point.size	Numeric value. Size of data points on reduced dimension space.
point.alpha	Numeric value. Transparency of the data points on reduced dimension space. Take any values between 0 to 1. The smaller the value, the more transparent the data points will be.
point.stroke	Numeric value. The thickness of the outline of the data points. The larger the value, the thicker the outline of the data points.
seed	Numeric value. Ensures imputed values for NA PSIs are reproducible.
method.impute	Character string. Indicate the method for imputing missing PSI values (low coverage). "random" method randomly assigns any values between 0-1. "population.mean" method uses the mean PSI value for each cell population. Default option is "population.mean".
cell.group.column.impute	Character string. Only applicable when method.impute set to "population.mean". The name of the sample metadata column in which the variables will be used to impute missing values.

Value

An object of class S3 containing with new slots MarvelObject$PCA$PSI$Results and MarvelObject$PCA$PSI$Plot

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

# Define splicing events for analysis
df <- do.call(rbind.data.frame, marvel.demo$PSI)
tran_ids <- df$tran_id

# PCA
marvel.demo <- RunPCA.PSI(MarvelObject=marvel.demo,
                          sample.ids=marvel.demo$SplicePheno$sample.id,
                          cell.group.column="cell.type",
                          cell.group.order=c("iPSC", "Endoderm"),
                          cell.group.colors=NULL,
                          min.cells=5,
                          features=tran_ids,
                          point.size=2
                          )

# Check outputs
head(marvel.demo$PCA$PSI$Results$ind$coord)
marvel.demo$PCA$PSI$Plot

MARVEL documentation built on Oct. 31, 2022, 5:07 p.m.