norm.tm.opt: Trimmed-Mean normalization optimized

Description Usage Arguments Value Author(s)

View source: R/norm.tm.opt.R

Description

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

Usage

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

Arguments

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.

Value

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

Author(s)

Jean Monlong


jmonlong/PopSV documentation built on April 19, 2018, 2:10 p.m.