#' @title recodedgen
#' @description sample genetic data
#' @details recodedgen is sample genetic data provided with the GARCOM package. It has with 10 rows and 16 columns.
#' Where the first 6 columns are FID, IID, PAT, MAT, SEX and PHENOTYPE which are inherent from the 
#' PLINK (recode) output. Columns followed by PHENOTYPE are SNP names which are suffixed with _A, or _C
#' or _T or _G. Each SNP column may have 0, 1, 2 or NA value. Where NA represents missingness.

"SEX"=c( c( c(rep(1,5)),rep(0,5))),
"PHENOTYPE"=c( c(rep("NA",2),rep("1",4),
"SNP8_C"=c(rep(0,10)), "SNP9_T"=c(rep(0,10)), "SNP10_A"=c(rep(0,10)))

#' @title snpgene
#' @description sample SNP-gene annotation data
#' @details snpgene is sample SNP-Gene annotation data provided with the GARCOM package. It has 10 rows and 2 columns. 
#' Column names are GENE and SNP, where GENE column contains GENE names and SNP column
#' contains SNP name that is annotated with the GENE


#' @title snppos
#' @description sample data for SNP coordinates
#' @details snppos is sample SNP-BP data provided with the GARCOM package. It has 2 columns and 10 rows. Column names are SNP and BP. 
#' where SNP columns contains SNP names BP column contains position of the SNP

snppos<-data.frame("SNP"=c(paste("SNP",seq(1:10),sep="")), "BP"=c(1100, 89200, 2500, 33000, 5500, 69500, 12000,8800, 23200, 27000))

#' @title genecoord 
#' @description sample data for gene base pair boundaries
#' @details genecoord is example data provided with the GARCOM package. It has 3 columns and 5 rows. 
#' Column names are GENE, START and END where GENE column contains gene name, START and END indicate 
#' start BP and end BP respectively.

sariya/GARCOM documentation built on Jan. 1, 2023, 8:29 a.m.