markOut: Display outlying expressions

In Huang-lab/oppti: Outlier Protein and Phosphosite Target Identifier

Display outlying expressions

Description

Mark outlying expressions on the scatter plot of a given marker

Usage

markOut(dat, dat.imp, dat.imp.test, dat.dys, dys.sig.thr.upp,
marker.proc.list = NULL, dataset = "", num.omit.fit = NULL,
draw.sc = TRUE, draw.vi = TRUE, conf.int = 0.95,
ylab = "Observed", xlab = "Inferred")

Arguments

dat	an object of log2-normalized protein (or gene) expressions, containing markers in rows and samples in columns.
dat.imp	the imputed data that putatively represents the expressions of the markers in the (matched) normal states.
dat.imp.test	marker's p-value of the statistical significance between its observed vs imputed values computed by the Kolmogorov-Smirnov test.
dat.dys	samples' distances to regression line (i.e., dysregulation) on the scatter plots.
dys.sig.thr.upp	the dysregulation score threshold to elucidate/mark significantly dysregulated outlier events.
marker.proc.list	character array, the row names of the data to be processed for outlier analyses and for plotting.
dataset	the cohort name to be used in the output files.
num.omit.fit	number of outlying events to ignore when fitting a marker's observed expressions to the imputed ones.
draw.sc	logical, to draw a scatter plot for every marker in marker.proc.list in a separate PDF file.
draw.vi	logical, to draw a violin plot for every marker in marker.proc.list in a separate PDF file.
conf.int	confidence interval to display around the regression line
ylab	a title for the y axis
xlab	a title for the x axis

Value

the scatter plots of the markers where the outlier dysregulation events are highlighted by red mark.

Examples

set.seed(1)
dat = setNames(as.data.frame(matrix(runif(10*10),10,10),
row.names = paste('marker',1:10,sep='')), paste('sample',1:10,sep=''))
dat.imp = artImpute(dat, ku=6)
dat.imp.test = statTest(dat, dat.imp)[[1]]
dat.dys = dysReg(dat, dat.imp)[[1]]
plots = markOut(dat, dat.imp, dat.imp.test, dat.dys, dys.sig.thr.upp = .25)

Huang-lab/oppti documentation built on March 26, 2023, 12:52 p.m.