markOut: Display outlying expressions

Description Usage Arguments Value Examples

View source: R/analyze.R

Description

Mark outlying expressions on the scatter plot of a given marker

Usage

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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

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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)

oppti documentation built on Nov. 8, 2020, 5 p.m.