calcFreqs: calcFreqs

In bertamiro/lpattern: Detection of scatterplots with L-shaped pattern

Description

calcFreqs Given two numeric vectors this function overimposes a grid on the scatterplot defined by YMet~Xmet #' and returns a 3X3 matrix of counts with the number of points in each cell of the grid #' for given vertical and horizontal lines.

Usage

calcFreqs(xMet, yExp, x1, x2, y1 = NULL, y2 = NULL, percY1 = 1/3,
  percY2 = 2/3)

Arguments

xMet	First numeric vector which, in principle, contains the methylation values.
yExp	Second numeric vector which, in principle, contains the expression values.
x1, x2	Coordinates of vertical points in the X axis. Because it is expected to contain methylation values that vary between 0 and 1 the default values are 1/3 and 2/3.
y1, y2	Coordinates of vertical points in the Y axis. Leaving them as NULL assigns them the percentiles of yVec defined by 'percY1' and 'percY2'.
percY1, percY2	Values used to act as default for 'y1'and 'y2' when these are set to 'NULL'

Examples

## Not run: 
data(trueGenes)
xVec<- as.numeric(myMetilData[trueGene1,])
yVec<-as.numeric(myExprData[trueGene1,])
titolT <- trueGene1
plotGeneSel(xMet=xVec, yExp=yVec, titleText=titolT, x1=1/3, x2=2/3)
messageTitle(paste("Cell counts for gene",trueGene1))
calcFreqs(xMet=xVec, yExp=yVec, x1=1/3, x2=2/3, y1=NULL, y2=NULL, percY1=1/3, percY2=2/3)

xVec<- as.numeric(myMetilData[falseGene1,])
yVec<-as.numeric(myExprData[falseGene1,])
titolF <- falseGene1
messageTitle(paste("Cell counts for gene",falseGene1))
plotGeneSel(xMet=xVec, yExp=yVec, titleText=titolF, x1=1/3, x2=2/3)
calcFreqs(xMet=xVec, yExp=yVec, x1=1/3, x2=2/3, y1=NULL, y2=NULL, percY1=1/3, percY2=2/3)

## End(Not run)

bertamiro/lpattern documentation built on July 19, 2019, 12:56 p.m.