getsnp: Read SNP data from a binary dosage file

In BinaryDosage: Creates, Merges, and Reads Binary Dosage Files

Description

Routine to read the dosage and genetic probabilities about a SNP from a binary dosage file

Usage

getsnp(bdinfo, snp, dosageonly = TRUE)

Arguments

bdinfo	Information about a binary dosage file return from getbdinfo
snp	The SNP to read the information about. This may be the SNP ID or the index of the SNP in the snps dataset in the bdinfo list
dosageonly	Indicator to return the dosages only or the dosages allowing with the genetic probabilities. Default value is TRUE

Value

A list with either the dosages or the dosages and the genetic probabilities.

Examples

# Get the information about the file
vcf1abdfile <- system.file("extdata", "vcf1a.bdose", package = "BinaryDosage")
bdinfo <- getbdinfo(bdfiles = vcf1abdfile)

# Read the first SNP
getsnp(bdinfo, 1, FALSE)

Example output

$dosage
 [1] 2.000 1.002 1.000 0.122 1.000 0.000 1.004 2.000 0.000 0.918 2.000 0.940
[13] 0.783 0.000 1.000 0.013 1.000 0.000 0.089 1.000 2.000 0.869 0.000 1.000
[25] 1.860 1.000 0.000 0.982 1.000 2.000 0.000 0.000 1.000 0.000 0.000 1.000
[37] 0.065 0.949 0.850 0.000 1.031 1.000 1.015 0.000 0.000 0.000 1.000 2.000
[49] 0.000 0.999 1.000 0.000 0.121 0.000 0.000 2.000 0.000 1.000 0.000 0.000

$p0
 [1] 0.000 0.000 0.000 0.878 0.000 1.000 0.000 0.000 1.000 0.082 0.000 0.060
[13] 0.217 1.000 0.000 0.987 0.000 1.000 0.911 0.000 0.000 0.145 1.000 0.000
[25] 0.000 0.000 1.000 0.018 0.000 0.000 1.000 1.000 0.000 1.000 1.000 0.000
[37] 0.935 0.051 0.150 1.000 0.000 0.000 0.000 1.000 1.000 1.000 0.000 0.000
[49] 1.000 0.001 0.000 1.000 0.882 1.000 1.000 0.000 1.000 0.000 1.000 1.000

$p1
 [1] 0.000 0.998 1.000 0.122 1.000 0.000 0.996 0.000 0.000 0.918 0.000 0.940
[13] 0.783 0.000 1.000 0.013 1.000 0.000 0.089 1.000 0.000 0.842 0.000 1.000
[25] 0.140 1.000 0.000 0.982 1.000 0.000 0.000 0.000 1.000 0.000 0.000 1.000
[37] 0.065 0.949 0.850 0.000 0.969 1.000 0.985 0.000 0.000 0.000 1.000 0.000
[49] 0.000 0.999 1.000 0.000 0.115 0.000 0.000 0.000 0.000 1.000 0.000 0.000

$p2
 [1] 1.000 0.002 0.000 0.000 0.000 0.000 0.004 1.000 0.000 0.000 1.000 0.000
[13] 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.014 0.000 0.000
[25] 0.860 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000
[37] 0.000 0.000 0.000 0.000 0.031 0.000 0.015 0.000 0.000 0.000 0.000 1.000
[49] 0.000 0.000 0.000 0.000 0.003 0.000 0.000 1.000 0.000 0.000 0.000 0.000

BinaryDosage documentation built on Jan. 13, 2020, 5:06 p.m.