codeHaplo {inveRsion} | R Documentation |
Codes haplotypes into decimal integers
Description
The function labels the haplotypes of size blockSize
around each candidate brake-point. For labeling genotype data, the function takes objects of class genoDat
as main argument. For phased data, this argument should be ignored and a file name passed instead.
Usage
codeHaplo(objectGenoDat, blockSize, minAllele, saveRes = TRUE, file = NULL, ROI,intSNP=FALSE,phasing="inversion&BP")
Arguments
objectGenoDat |
Genodat object; if phased data then provide file instead
|
blockSize |
numeric . number of SNPs flanking each side of each candidate brake-point. Default value 3
|
minAllele |
numeric . minimum allele frequency for each probe to be considered as a candidate brake-point. Default value 0.1
|
saveRes |
logical . Whether results should be saved in file hapCode.RData
|
file |
character . File name with phased data
|
ROI |
numeric . 2-vector specification passes a chromosome segment to be encoded. 4-vector specification passes the region of interest for the left brake-point (ROI[1] and ROI[2]) and the right brake-point (ROI[3] and ROI[4])
|
intSNP |
logical . whether build flanking blocks of uniform SNP density across the genome.
|
phasing |
character . Either c("ivenrsion&BP","forward", "forward&inverted"), defines the phasing strategy between all four flanking blocks of each break poin. ivenrsion&BP phases the internal flanking block first, then the external blocks to the internal bloks and match them. "forward" uses the blocks in the sequence assumming the forward population; in the inversion model, the backward population is obtained inverting the internal blocks. "forward&inverted" phases the forward and inverted population independently.
|
Details
When setUpGenodat
is passed, the coding first computes the local haplotypes for each candidate-brake point form the genotype data and then encodes each haplotype into a decimal integer. The local haplotypes are computed with haplo.em
form haplo.stats
and assigns those with highest posterior probability to each chromosome. In the case of phased data, passed through file
, no local haplotyping is needed and only the labeling is performed.
Value
Object of class HaploCode
Author(s)
Alejandro Caceres acaceres@creal.cat
References
http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
See Also
GenoDat
, HaploCode
,
Examples
data(gDat)
hapCode <-codeHaplo(gDat,blockSize=3,minAllele=0.3,saveRes=FALSE)
hapCode
[Package
inveRsion version 1.41.0
Index]