Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/combineScores.R

Combine several similarities into one using several methods.

1 2 3 4 | ```
combineScores(scores, method = c("max", "avg", "rcmax", "rcmax.avg",
"BMA", "reciprocal"), round = FALSE, t = 0)
combineScoresPar(scores, method, subSets = NULL, BPPARAM = NULL, ...)
``` |

`scores` |
Matrix of scores to be combined |

`method` |
one of |

`round` |
Should the resulting value be rounded to the third digit? |

`t` |
Numeric value to filter scores below this value. Only used in the reciprocal method. |

`subSets` |
List of combinations as info in other functions. |

`BPPARAM` |
BiocParallel back-end parameters.
By default ( |

`...` |
Other arguments passed to |

The input matrix can be a base matrix or a matrix from package Matrix. The methods return:

- avg
The average or mean value

- max
The max value

- rcmax
The max of the column means or row means

- rcmax.avg
The sum of the max values by rows and columns divided by the number of columns and rows

- BMA
The same as

`rcmax.avg`

- reciprocal
The double of the sum of the reciprocal maximal similarities (above a threshold) divided by the number of elements. See equation 3 of the Tao

*et al*2007 article

A numeric value as described in details.

`combineScores`

is a version of the function of the same name in
package GOSemSim (`combineScores`

) with optional
rounding and some internal differences.

Lluís Revilla based on Guangchuang Yu

Ying Tao, Lee Sam, Jianrong Li, Carol Friedman, Yves A. Lussier; Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics 2007; 23 (13): i529-i538. doi: 10.1093/bioinformatics/btm195

register in BiocParallel about the arguments accepted by BPPARAM

1 2 3 4 5 6 7 8 9 10 11 12 | ```
(d <- structure(c(0.4, 0.6, 0.222222222222222, 0.4, 0.4, 0, 0.25, 0.5,
0.285714285714286), .Dim = c(3L, 3L),
.Dimnames = list(c("a", "b", "c"), c("d", "e", "f"))))
e <- d
sapply(c("avg", "max", "rcmax", "rcmax.avg", "BMA", "reciprocal"),
combineScores, scores = d)
d[1,2] <- NA
sapply(c("avg", "max", "rcmax", "rcmax.avg", "BMA", "reciprocal"),
combineScores, scores = d)
colnames(e) <- rownames(e)
combineScoresPar(e, list(a= c("a", "b"), b = c("b", "c")),
method = "max")
``` |

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