scoreGenesMat: scoreGenesMat

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

Description

scoreGenesMat scores scatterplots using a binary and a numeric schemes on a row-wise basis.

Usage

scoreGenesMat(mets, expres, x1 = 1/3, x2 = 2/3, y1 = NULL,
  y2 = NULL, percY1 = 1/3, percY2 = 2/3, aReqPercentsMat,
  aWeightMifL, aWeightMifNonL)

Arguments

mets	Matrix of methylation values
expres	Matrix of 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'
aReqPercentsMat	Matrix of minimum maximum percentage of counts to have in a given cell
aWeightMifL	A matrix of weights to score the previous counts if the scatterplot has been classified as L.
aWeightMifNonL	A matrix of weights to score the previous counts if the scatterplot has been classified as non-L
trace	logical. Set to TRUE to print count matrices as they are computed

Examples

## Not run: 
sampleSize <- dim(mets)[2]
numGenes <-   dim(mets)[1]
reqPercentages <- matrix (c(2, 20, 5, 1, 40, 20, 0, 1, 2), nrow=3, byrow=TRUE)
(theWeightMifL=matrix (c(2,-2,-sampleSize/5,1,0,-2,1,1,2), nrow=3, byrow=TRUE))
(theWeightMifNonL=matrix (c(0,-2,-sampleSize/5,0,0,-2,0,0,0), nrow=3, byrow=TRUE))
scoreGenesMat <- function(mets, expres,
                         x1=1/3, x2=2/3,
                         y1=NULL, y2=NULL, percY1=1/3, percY2=2/3,
                         aReqPercentsMat = reqPercentages,
                         aWeightMifL= theWeightMifL,
                         aWeightMifNonL= theWeightMifNonL) # , trace=FALSE)
## End(Not run)

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