read a LINKAGE pedigree file into a snp.matrix object
reads post-MAKEPED pedigree files (used by JPSGCS)
The post-MAKEPED format includes nine columns of pedigree structure and
subject characteristics (see Details below)
before the marker data. By contrast, pre-MAKEPED
pedigree file format has only six column of pedigree and subject data
before the marker data. This function was adapted from the
in the chopsticks package (formerly
snpMatrix), which reads pre-MAKEPED pedigree files.
The name of the pedigree file to be read.
A character vector of SNP names. If
A list of named mappings from letters to alleles; not currently used.
Missing data code in the pedigree file; not currently used.
Is the pedigree file comprised of X-chromosome SNPs? Default is
Character string to separate Family and Member IDs in the row.names of
JPSGCS pedigree files are in post-MAKEPED format (though much of this information is ignored):
|Column 1:||Pedigree number|
|Column 2:||Individual ID number|
|Column 3:||ID of father; 0=no father in pedigree|
|Column 4:||ID of mother; 0=no mother in pedigree|
|Column 5:||First offspring ID; ignored by JPSGCS|
|Column 6:||Next paternal sibling ID; ignored by JPSGCS|
|Column 7:||Next maternal sibling ID; ignored by JPSGCS|
|Column 8:||Sex; 1=male, 2=female|
|Column 9:||Proband status (1=proband, 0=not); ignored by JPSGCS|
The pre-MAKEPED format excludes columns 5 - 7.
read.pedfile is essentially
read.snps.pedfile for post-MAKEPED
pedigree files, except that the option
has not been implemented.
read.snps.pedfile, when reading in SNP genotype data
the function looks for a corresponding
.info file with information on the SNPs such
as physical map positions. For example, if
the function looks for
test.info to read
SNP information. Any SNP information that is found is saved in
snp.support of the output object (see Value).
A list with three components:
a data frame containing the first nine columns of the pedigree file, and
a data frame of SNP information. NB: this is
only meaningful if a
Sigal Blay, Jinko Graham and Brad McNeney
The JPSGCS webpage description of how the LINKAGE pedigree file format is used may be found at http://balance.med.utah.edu/wiki/index.php/LINKAGE
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