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####################################################################
## Author: Gro Nilsen, Knut Liestřl and Ole Christian Lingjćrde.
## Maintainer: Gro Nilsen <gronilse@ifi.uio.no>
## License: Artistic 2.0
## Part of the copynumber package
## Reference: Nilsen and Liestřl et al. (2012), BMC Genomics
####################################################################
#Get arm numbers from chromosomes, position and cytoband data:
##Input:
### chrom: vector of chromosome numbers
### pos: vector of positions
### pos.unit: unit for positions
### cyto.data: object specifying which genome assembly version should be used for cytoband data
##Output:
### arms: a character vector with arms; dentoed p and q
##Required by:
### adjustPos
### multipcf
### pcf
### winsorize
### aspcf
##Requires:
### getArmandChromStop
### numericChrom
getArms <- function(chrom, pos, pos.unit="bp", cyto.data){
#Make sure chromosomes are numeric:
chrom <- numericChrom(chrom)
nProbe <- length(chrom)
chrom.list <- unique(chrom)
nChrom <- length(chrom.list)
#Get local stopping posistions for each p-arm and each chromosome from cytoband data
l <- getArmandChromStop(cyto.data=cyto.data,unit=pos.unit)
pStop <- l$pstop
chromStop <- l$chromstop
#Intitialize
arms <- rep(NA,nProbe)
for(i in 1:nChrom){
#Find corresponding arm numbers:
c <- chrom.list[i]
ind.c <- which(chrom==c)
arms[ind.c] <- "q"
p.arm <- ind.c[pos[ind.c]<=pStop[c]]
arms[p.arm] <- "p" #p-arm
}
return(arms)
}
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