vcfs_all: Data to use as input to the applyTMB functions in tests

In acc-bioinfo/TMBleR: Tumor Mutational Burden Quantification From Gene Panels And WES

Description

List of lists, , generated by applyFilters or applyInputToTMB, containing required input to the applyTMB function. Each element of the list corresponds to a sample and is a list with the following elements: sample, filter, variants and design.

Usage

vcfs_all

Format

A data frame with 4 rows and 5 variables

sample

character, sample identifier

Filter

character, type of filter, if any, applied on input mutations

design

GRanges object, regions targeted by the sequencing experiment (WES or Panel)

variants

data.frame, describing mutations by chromosome, start and end coordinates, REF and ALT alleles

Source

generated in house as an example of TMB estimated obtained by WES.

acc-bioinfo/TMBleR documentation built on Dec. 18, 2021, 10:21 p.m.