bed.matrix.split.genomic.region: Bed matrix for variants associated to multiple genomic...

In Ravages: Rare Variant Analysis and Genetic Simulations

Bed matrix for variants associated to multiple genomic regions

Description

Creates a new bed matrix with variants associated to multiple genomic regions being duplicated

Usage

bed.matrix.split.genomic.region(x, changeID=TRUE, genomic.region=NULL, 
                                split.pattern=",")

Arguments

x	A bed.matrix
changeID	TRUE/FALSE: whether to change the variants ID by including the gene name
genomic.region	A vector containing the genomic region of each variant
split.pattern	The character separating the genomic regions

Details

If changeID=TRUE, variants will have new IDs being CHR:POS:A1:A2:genomic.region.

The genomic region(s) associated to each varaint should be in x@snps$genomic.region or given as a vector to genomic.region. If both are present, genomic.region is used.

Value

A bed matrix with variants assigned to multiple genomic regions being duplicated and the corresponding genomic regions separated and transformed into factors.

Examples

#Example bed matrix with 4 variants
  x.ex <- as.bed.matrix(x=matrix(0, ncol=4, nrow=10), 
                       bim=data.frame(chr=1:4, id=paste("rs", 1:4, sep=""), dist = rep(0,4), 
                                      pos=c(150,150,200,250), A1=rep("A", 4), A2=rep("T", 4)))

#Example genes dataframe
  genes.ex <- data.frame(Chr=c(1,1,3,4), Start=c(10,110,190,220), End=c(170,180,250,260), 
                         Gene_Name=factor(letters[1:4]))

#Attribute genomic regions
  x.ex <- set.genomic.region(x.ex, regions = genes.ex)

#Split genomic regions
  x.ex.split <- bed.matrix.split.genomic.region(x.ex, split.pattern = ",")

Ravages documentation built on April 1, 2023, 12:08 a.m.