dnds: Run a dN/dS analysis on MOBSTER clusters.

In caravagnalab/mobster: MOBSTER - Model-based tumour subclonal deconvolution

Run a dN/dS analysis on MOBSTER clusters.

Description

This function takes a MOBSTER fit and runs 'dndscv' (https://github.com/im3sanger/dndscv) to calculate dN/dS values per cluster. It computes global dN/dS and per gene dN/dS values and makes a plot. dN/dS values are computed with the best fitting MOBSTER model.

Usage

dnds(
  x,
  mapping = NULL,
  gene_list = NULL,
  colors = c(Tail = "gray"),
  refdb = "hg19",
  dndscv_plot = c("wall", "wmis", "wnon", "wspl", "wtru"),
  ...
)

Arguments

x	A MOBSTER fit object.
mapping	The groups used to compute this statistics are defined by this variable. If ‘mapping = c('A' = ’G1', ‘B' = ’G1', ‘C' = ’G2')', then mutations from clusters 'A' and 'B' will be pooled into one group ('G1'), while mutations from cluster 'C' will constitute a group themselves. By default, with 'mapping = NULL', each cluster is a group.
gene_list	An optional vector of gene names to infer dN/dS values, default ('NULL') is to use dndscv default (whole-exome. This package provides lists genes that can be used for this value (essential genes, cancer genes, etc.); see package data.
colors	If provided, these colours will be used for each cluster. If a subset of colours is provided, palette Set1 from RColorBrewer is used. By default the tail colour is provided as 'gainsboro'.
refdb	The genome referene to use, default is to use hg19. Other references are available from https://github.com/im3sanger/dndscv_data
dndscv_plot	What of the dndscv scores should be visualized in a plot, by default all the statistcs are reported. One can use 'dndscv_plot = wall' to get only the global dnds value.
...	Extra parameters forwarded to dndscv.

Value

The fit object is a list with the summary table and the observation counts reported by package dndscv, together with a ggplot plot for the results.

Examples

# Example run with real data
data('LUFF76_lung_sample', package = 'mobster')

clusters = Clusters(LUFF76_lung_sample$best)

dnds_stats = dnds(clusters, gene_list = NULL)

caravagnalab/mobster documentation built on March 25, 2023, 3:40 p.m.