Downsample a whole exome sequencing (WES) dataset to a subset only containing genes targeted in the panel

This function calls the simulatePanel function on a list of inputs and for each element of the list it generates a subset of a whole exome sequencing dataset which only includes the genes of a given gene panel. This subset may then be used to simulate panel-based TMB quantification.

applySimulatePanel(WES, WES.design, panel.design, assembly)

Arguments

WES	a list generated by applyFilters or applyInputToTMB with variants, filter, design and sample elements.
WES.design	a GRanges object containing WES sequencing design. Used to remove off target mutations
panel.design	a GRanges object containing sequencing design of the panel tyou want to simuate. Used to subset WES.
assembly	human genome assembly: "hg19" or "hg38"

Value

Returns a list of lists (one for each element of the input list). Each list contains variants, filter, design and sample elements. The variants element is a GRanges object containing variants from the simulated panel, which is only those variants from WES falling in the regions targeted by the panel

Author

Laura Fancello

Examples

## Read design
# Load the design of the WES
data(ExampleWESdesign)

# Load the design of the gene panel that you want to simulate
data(ExamplePaneldesign)

# Load input to applySimulatePanel function
data(vcfs_NoCancer_ForPanel)

# Subset WES dataset, provided as GRanges object so that it will only contain
# variants in the regions targeted by the panel you want to simulate
SimulatedPanel_NoCancer <- applySimulatePanel(WES = vcfs_NoCancer_ForPanel
, WES.design = ExampleWESdesign
, panel.design= ExamplePaneldesign 
, assembly = "hg19")