Description Usage Arguments Value Author(s)

Optimized version of the trimmed-mean normalization for bin counts.

1 2 | ```
norm.tm.opt(df, ref.col, lm.min.prop = 0.1, bc.mean.norm = NULL,
chrs = NULL)
``` |

`df` |
a data.frame with the bin counts (bin x sample). |

`ref.col` |
the column to be used as baseline for the pairwise normalization. All columns are normalized on this sepcified column. |

`lm.min.prop` |
the minimum height proportion in the density curve to define a local maximum. |

`bc.mean.norm` |
the average coverage in the reference sample. To be used to help normalize tumor samples. |

`chrs` |
the chromosomes of the bins used. The diversity of the chromosome is useful to differentiate misleading coefficient from a few aberrant chromosomes. |

a vector with the normalization coefficients for each column (sample).

Jean Monlong

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