LoadAnnovar: Load data from annovar-annotated variant calls.

In rahuldhodapkar/melange: Multi-Modal Data Import Utilities for Seurat

Description

LoadAnnovar loads Annovar data for the provided cell to file mapping. By default, does not perfom any quality control on variant call files. LoadAnnovar should be provided *.variant_function files for each cell. If additional exonic functional pruning is required, LoadAnnovar will automatically extract the location of the corresponding *.exonic_variant_function file locally.

Usage

LoadAnnovar(cells, annovar.filenames, germline.filename,
  reduction = "by_gene", somatic.only = TRUE, exonic.only = TRUE,
  read.depth.norm.col = 10, spike.in.regex = "^ERCC-",
  unique.id.cols = c(3, 4, 5, 6, 7))

Arguments

cells	character vector containing cell IDs
annovar.filenames	character vector containing annovar file paths.
germline.filename	file path for annovar file containing germline variants. Used as a positive control for single-cell somatic variant analysis.
reduction	reduction to use from annovar to Seurat assay. Currently 'by_gene'
somatic.only	boolean, default TRUE, produce counts based only on predicted somatic variants (subtact germline)
exonic.only	boolean, default TRUE, produce counts based only on variants predicted to occur within exons.
read.depth.norm.col	default 10, col with read depth to normalize variant calls by for single cell analysis. If using the default Annovar conversion tools from VCF, this will most likely be column 10.
spike.in.regex	regex selection for 'CHR' vcf field inidcating synthetic spike-in. Used as a negative control for single-cell somatic variant analysis. Default '^ERCC-'
unique.id.cols	set of columns that uniquely define a variant in the *.variant_function file. Will be used to generate row names for the final aggregated data set.

Value

A matrix containing the reduced counts of each ENSG merged from all cells supplied in a Seurat-importable format.

Examples

## Not run: 

LoadAnnovar(c('1', '2'),
    c('1.anno.variant_function', '2.anno.variant_function')
)


## End(Not run)

rahuldhodapkar/melange documentation built on Nov. 5, 2019, 2:07 a.m.