variants_power: Compute sensitivity and specificity for the a set of variants...

In annaquaglieri16/samplepower: Compute sensitivity and false positive rates for a variant call set with repsect to a truth dataset.

Description

Compute sensitivity and specificity for the a set of variants with respect to some truth sets

Usage

variants_power(variant_files, variant_files_initial, down_label = NA,
  truth_set = NA, caller, gene_expression = NA, normal_variants,
  exon_ranges, homop_ranges, RNAedit_ranges, repeats_ranges, ncbi,
  flag_patterns, path_to_gatk_coverage, TCGA = FALSE)

Arguments

variant_files	character vector containing the paths to all the tab delimited files of variants from the downsampled run. See details.
variant_files_initial	character vector containing the paths to all the tab delimited files of variants from the initial run with deeply sequenced RNA-Seq samples. See details.
down_label	character. Any label to be assigned to the current run
truth_set	external truth set
caller	one of 'varscan', 'mutect' or 'vardict'
gene_expression	if available, 'rds' objects with raw gene expression data where rows are genes and columns are samples
normal_variants	link to panel of normal file parsed with 'samplepower::parse_pon'
exon_ranges	GRanges object with exon boundaries relative to the reference genome used
homop_ranges	GRanges object with homopolymers regions of more than 5bp relative to the reference genome used
RNAedit_ranges	GRanges object with RNA editing sites relative to the reference genome used
repeats_ranges	GRanges object with repetitive regions of the reference genome used
ncbi	NCBI annotation dataframe including at least the columns 'GeneID' and 'Symbol'
flag_patterns	dataframe containing the flags to assign to variants. THIS NEEDS TO BE SET AS INTERNAL TO THE PACKAGE
path_to_gatk_coverage	path to file where the GATK 'DepthOfCoverage' output is saved
TCGA	logical. If TRUE variants will be macthed with truth sets excluding transcript information

Details

The files whose links are recorded in 'variant_files_initial' and 'variant_files' are the ouput files obtained with the 'call_variants.R' function from the functions in https://github.com/annaquaglieri16/RNA-seq-variant-calling#panel-of-normals-pon. The VCF output from every callers are standardised to make the results easily comparable across callers.

annaquaglieri16/samplepower documentation built on Nov. 7, 2019, 11:43 p.m.