View source: R/create.ibd.dat.q
create.ibd.dat | R Documentation |
Combine a posterior IBD probabilities file with a prior IBD probabilities file
create.ibd.dat(postfile, priorfile, software="merlin", x.linked=FALSE, cov.data=NULL, rm.noninform=TRUE)
postfile |
full path and name of the file with posterior IBD probabilities |
priorfile |
full path and name of the file with prior IBD probabilities |
software |
character string of which software was used to create IBD probability files |
x.linked |
logical, is the chromosome X-linked. If TRUE, cov.data is required |
cov.data |
name of data.frame containing covariates, specifically ped.id, person.id, and sex. Required when x.linked=TRUE. |
rm.noninform |
logical, if TRUE, remove relative pairs that are not informative for linkage |
Perl scripts are provided within ibdreg/perl/ for creating IBD probability files, and are explained in the user manual. Prior probability files are made using a homozygous marker on the pedigree structure, or a "dummy" marker. When the chromosome is X-linked, the Merlin software treats males as homozygous for their X chromosome, and thus the probability of sharing 1 and 2 alleles IBD with any other relative are switched within create.ibd.dat.
An object with class ibd.dat, which contains the following elements:
ped.id |
pedigree identifier code |
person1.id |
identifier to person 1 of the relative pair |
person2.id |
identifier to person 2 of the relative pair |
post0 |
data.frame with probability of sharing zero (0) alleles ibd between relative pairs (rows) at each position (columns) |
post1 |
data.frame with probability of sharing one (1) alleles ibd between relative pairs (rows) at each position (columns) |
post2 |
data.frame with probability of sharing two (2) alleles ibd between relative pairs (rows) at each position (columns) |
prior0 |
vector with probability of sharing zero (0) alleles ibd between relative pairs, given no genotype data |
prior1 |
vector with probability of sharing one (1) alleles ibd between relative pairs, given no genotype data |
prior2 |
vector with probability of sharing two (2) alleles ibd between relative pairs, given no genotype data |
ibdreg
,
ibd.df.merlin
,
mergeIBD
## do not run example in testing ## uncomment to run for demo ## ibd file for 1 chromosome # ibdfile.ch20 <- "post.ibd" ## ibd file for 1 locus for prior probs. # prior.ibdfile <- "prior.ibd" # ibd.dat.obj <- create.ibd.dat(postfile=post.ibd, # priorfile=prior.ibd, # rm.noninform=FALSE) # names(ibd.dat.obj)
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