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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.
You can install the released version of GARCOM from CRAN with:
install.packages("GARCOM")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 manualcitation("GARCOM")data.table(>=v1.12.8)
stats
vcfR(>=v1.12.0)testthatGARCOM welcomes suggestions and improvements. Please open issues on the github for bugs/suggestions.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! - Add support for Bgen format
- Add support for functional annotation (synonymous, non synonymous, etc.) in the VCF dataCurrently v1.2.0These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.