GARCOM

install.packages("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("GARCOM")