# 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

 ```1 2 3``` ```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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13``` ```## 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.