Description Usage Arguments Examples

View source: R/scoreGenesMat.R

`scoreGenesMat`

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

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)
``` |

`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 |

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)
``` |

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