mutation-handler: From maf format prepare the mutation table

In cavei/pancancerPreprocessing: Encapsulate basic function to process pancancer dataset

Description

From maf format prepare the mutation table

Collapse mutations Given the same gene and patients mutation impact and type are collapsed.

Select mutation by type

Select mutation by impact

Usage

prepareMutations(maf, impact = NULL, mutType = NULL,
  filterByThisEntrez = NULL, patients = NULL, select_type = TRUE,
  tumor_site_type = "01", select_columns = c(hugo = 1, entrez = 2,
  impact = 94, type = 9, patient = 16))

summarizeMutation(smallMaf)

selectMutation(smallMaf, type)

selectImpact(smallMaf, type)

Arguments

maf	a maf format table
impact	select by impact
mutType	select by mutation type
filterByThisEntrez	filter to keep only entred listed
patients	keep only the patients listed
select_type	logical to perform selection on the type
tumor_site_type	keep only tumor samples of the type. 01 primary solid tumor.
select_columns	named numeric to specyfy the columns to select
smallMaf	reduced version of a maf file
type	mutation type

Value

a matrix entrez x samples

smallMaf subset (matrix or data.frame)

cavei/pancancerPreprocessing documentation built on Nov. 4, 2019, 8:46 a.m.