linkdat(ped, model=NULL, map=NULL, dat=NULL, freq=NULL, verbose=TRUE,
missing=0, ...)
## S3 method for class 'linkdat':
print(x, ..., markers)
## S3 method for class 'linkdat':
summary(object, ...)
## S3 method for class 'linkdat':
as.data.frame(x, ..., famid=F, markers=seq_len(x$nMark),
alleles=NULL, missing=NULL, singleCol=FALSE, sep="")
## S3 method for class 'linkdat':
subset(x, subset=x$orig.ids, ..., markers=seq_len(x$nMark))
write.linkdat(x, prefix="", what=c("ped", "map", "dat", "freq", "model"),
merlin=FALSE)
linkdat.model
object (typically y$model
for some linkdat object y
), or a single integer with the following meaning:
1 = autosomal dominant; 2 = autosomal recessive; 3 = X-linked dominant; 4 = X-linked recemap
is non-NULL.)linkdat
object.alleles=c("A","B")
.singleCol=TRUE
.prefix="fam1"
and what=c("ped", "map")
, the files "fam1.ped" and "fam1.map" will be created.linkdat
object, or a list of linkdat
objects. A linkdat object is essentially a list with the following entries, some of which can be NULL.data.frame
with 5 columns (ID, FID, MID, SEX, AFF) describing the pedigree in linkage format. (NB: Internal labeling used.)marker
objects.linkdat.model
object, essentially a list containing the model parameters. See setModel
for details.ped
must describe one or several pedigrees in standard LINKAGE format, i.e. with the following columns in correct order:
1 Family id (optional) (FAMID)
2 Individual id (ID),
3 Father id (FID),
4 Mother id (MID),
5 Gender (SEX): 1 = male, 2 = female,
6 Affection status (AFF): 1 = unaffected, 2 = affected, 0 = unknown,
7 First allele of first marker,
8 Second allele of first marker,
9 First allele of second marker,
a.s.o.
Only columns 2-6 are mandatory. The first column is automatically interpreted as family id if it has repeated elements.
Internally the individuals are relabeled as 1,2,..., but this should rarely be of concern to the end user. Some pedigree checking is done, but it is recommended to plot the pedigree before doing any analysis.
Details on the formats of map, dat and frequency files can be found in the online MERLIN tutorial: setModel
, modifyPedigree
, linkdat.utils
data(toyped)
toyped
x = linkdat(toyped, model=1)
x
summary(x)
# test read/write:
x = modifyMarker(x, 1, alleles=c('B','C'), afreq=c(.9, .1), chrom=2, name="SNP1", pos=123)
write.linkdat(x, prefix="toy")
y = linkdat("toy.ped", map="toy.map", dat="toy.dat", freq="toy.freq", model=1)
unlink(c("toy.ped", "toy.map", "toy.dat", "toy.freq", "toy.model"))
stopifnot(isTRUE(all.equal(x,y)))
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