bed.matrix.split.genomic.region {Ravages} | R Documentation |
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 = ",")
[Package Ravages version 1.1.3 Index]