mkMutProfileGeneCnv: Add annotations to the gene cnv table

In luannnguyen/hmfGeneAnnotation: Determines gene amplifications and biallelic losses from HMF pipeline output

Description

Annotations deep deletions, truncations, LOH, and amplifications

Usage

mkMutProfileGeneCnv(
  gene.cnv,
  arm.ploidies,
  min.cn.arm.ploidy.diff = 0.8,
  deep.del.max.max.copy.number = 0.3,
  trunc.max.min.copy.number = 0.3,
  loh.max.min.minor.allele.ploidy = 0.2,
  scoring = list(deep_deletion = c(5, 5), trunc = c(5, 5), loh = c(5, 0)),
  trunc.is.deep.del = T,
  verbose = T
)

Arguments

gene.cnv	purple gene cnv dataframe
arm.ploidies	arm ploidies dataframe
min.cn.arm.ploidy.diff	Minimum difference between min_copy_number and arm_ploidy before a gain is considered to have happened
deep.del.max.max.copy.number	The max max_copy_number for a gene to be considered to be completely lost (deep deletion)
trunc.max.min.copy.number	The max min_copy_number to for a gene to be considered to have a truncation
loh.max.min.minor.allele.ploidy	The maximum min_minor_allele_ploidy for a gene to be considered to have loss of heterozygosity
scoring	a list in the form list(deep_deletion=c(5,5),trunc=c(5,5),loh=c(5,0))
trunc.is.deep.del	Consider truncations the same as deep deletions?

Value

The original input dataframe with annotation columns

luannnguyen/hmfGeneAnnotation documentation built on May 6, 2020, 1:07 p.m.