Gene and Region Counting of Mutations ("GARCOM").

GARCOM

The goal of GARCOM is to provide mutation counts per individual within genetic boundaries (genes). It accepts different data formats with input file from plink (.raw), gene boundaries, SNP location. It also accepts VCF file format. The vcf file is assumed to be pVCF, that is where all samples are merged/combined.

Installation

You can install the released version of GARCOM from CRAN with:

install.packages("GARCOM")

Example

This is a small example which shows you how to use GARCOM:

library(GARCOM)
## basic example code
## sample data provided with library: genecoord, snpgene, snppos and genecoord

## Input data requires output from PLINK --recode flag. plink --bfile input --recode A --out sample_output 

#input data: .raw formatted and SNP-gene (two columns)
gene_annot_counts(recodedgen,snpgene) 

#input data: .raw formatted, SNP location (two columns) and Gene boundaries (three columns)
gene_pos_counts(recodedgen, snppos, genecoord) 

#read VCF file vcf_data <- vcfR::read.vcfR("CHRXX.vcf.gz", verbose=TRUE)
vcf_counts_annot(vcf_data,df_snpgene) # pass vcf data read and data frame with SNP-gene annotation

#read VCF file vcf_data <- vcfR::read.vcfR("CHRXX.vcf.gz", verbose=TRUE)
vcf_counts_SNP_genecoords(vcf_data,df_snppos,df_genecoords) # pass vcf data read and data frame SNP position and third with gene coordinates

#subset individuals 
vcf_counts_SNP_genecoords(vcf_data,df_snptestpos, df_genecoordstestpos,keep_indiv=c("IID1","IID2"))

ind_select<-c("IID1","IID2") ## store in a vector
vcf_counts_SNP_genecoords(vcf_data,df_snptestpos, df_genecoordstestpos,keep_indiv=ind_select)

## Filter individuals and filter genes for a VCF data
vcf_counts_SNP_genecoords(vcf_data,df_snptestpos,df_genecoordstestpos,keep_indiv=c("IID1","IID2"),filter_gene="GENE_1") #returns a matrix of data.table class

##For more examples refer manual

Citation

citation("GARCOM")

Dependencies (Imports)

data.table(>=v1.12.8)
stats
vcfR(>=v1.12.0)

suggests

testthat

Issues and suggestions

GARCOM welcomes suggestions and improvements. Please open issues on the github for bugs/suggestions.

Origin

GARCOM's derived from French word garçom (/ɡaʁ.sɔ̃/) 
GARCOM is ready to serve and obtain desired results for the genetics data. We hope you enjoy it! 

To-Dos

- Add support for Bgen format
- Add support for functional annotation (synonymous, non synonymous, etc.) in the VCF data

Version

Currently v1.2.0