norm.tm.opt: Trimmed-Mean normalization optimized

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

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

Usage

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 Sept. 15, 2019, 9:29 p.m.