sortSNPs: Sort a vector of SNPs by genomic position

In SNPassoc: SNPs-Based Whole Genome Association Studies

Sort a vector of SNPs by genomic position

Description

This function sorts a vector with the position of SNPs in a data frame using another data frame which contains information about SNPs, their chromosome, and their genomic position

Usage

sortSNPs(data, colSNPs, info)

Arguments

data	a required data frame with the SNPs
colSNPs	a required vector indicating which columns of 'data' contains genotype data
info	a required data frame with genomic information for the SNPs (chromosome and position). The first column must have the SNPs, the second one the chromosome and the third one the genomic position.

Details

First of all, the function obtains a vector with the SNPs sorted using the data frame with the genomic positions (see 'dataSNPs.pos' argument). Then, the columns which indicate where the information about the genotypes is in our data frame, are sorted using this vector.

This information is useful when WGassociation function is called since it allow the user to summaryze the results with the SNPs sorted by genomic position

Value

a vector indicating the colums where the SNPs are recorded in our data frame ('data' argument), sorted using the genomic positions listed in 'dataSNPs.pos' argument)

Examples

#
# data(SNPs)
# data(SNPs.info.pos)
# colSNPs.order<-sortSNPs(SNPs,c(6:40),SNPs.info.pos)
#

SNPassoc documentation built on Oct. 30, 2024, 9:26 a.m.