Usage
haplinTDT(filename, nsim.perm = 0, select.gender = NULL,
method = c("tdt", "hhrr", "trimm"), names.marker = NULL,
use.haplotypes = FALSE, use.ambiguous = TRUE, design = "triad",
markers = "ALL", n.vars = 0, sep = " ", allele.sep = ";",
na.strings = "NA", use.missing = FALSE, xchrom = FALSE,
sex = NULL, threshold = 0.01, verbose = TRUE, printout = TRUE)Arguments
Of the following arguments, only filename is required. Use of the remaining arguments will depend on the type of analysis.
filename
A character string giving the name and path of
the ASCII data file to be read.
nsim.perm
Number of permutations. Default is 0, which means that haplinTDT does not do
a permutation test.
select.gender
Do the analysis for a gender subset. Values: 1, 2, or NULL.
1: Male, 2: Female, NULL: All. Default is NULL.
method
A character vector containing the methods that are used
int the analysis. Possible values are "tdt", "hhrr" and
"trimm". Default are all three.
names.marker
Marker names. Default is NULL which means that the
markers are denoted 1, 2, ..., # markers.
use.haplotypes
A logical value, default is FALSE. If
use.haplotypes=TRUE haplotypes corresponding to the individual
markers are reconstructed by haplin using the EM
algorithm.
The haplotypes are then
use.ambiguous
A logical value, default is TRUE. If FALSE then
we remove those family triads where it is ambiguous which allele is
transferred to the child from a parent.
design
For the moment only the value "triad" is allowed. It is used for the standard case triad
design, without independent controls.
markers
Default is "ALL", which means haplinTDT uses all
available markers in the data set in the analysis. If
use.haplotypes = TRUE then for the current
version of haplin th n.vars
Numeric. The number of variables (columns) in the data
file before (to the left) of the genetic data.
sep
The character separator used in the data file to separate
between "columns", where each column contains the two alleles of a
single individual at a single marker.
allele.sep
The character separator used in the data file to
separate the two alleles for a single individual in a single
marker. The recommended (default) separator is ";", but for SNPs an
empty "" is also common.
na.strings
The character string indicating missing data in the
data file. Default is to use "NA" in place of, for instance, C;T for
a SNP that hasn't been typed in that individual.
use.missing
A logical value used to determine whether triads
with missing data should be included in the analysis. When set to
TRUE, haplinTDT uses haplin to xchrom
Logical, defaults to "FALSE". If set to "TRUE",
haplinTDT assumes the markers are on the x-chromosome. This option
should be combined with specifying the sex argument.
sex
A numeric value specifying which of the data columns that
contains the sex variable. The variable should be coded 1 for males
and 2 for females. To be used with xchrom = TRUE.
threshold
Sets the (approximate) lower limit for the haplotype
frequencies of those haplotypes that should be retained in the
analysis. Hapotypes that are less frequent are removed, and
information about this is given in the output.
verbose
Default is T (=TRUE).
printout
Logical. If TRUE (default), haplinTDT prints a full
summary of the results after finishing the estimation. If FALSE, no
such printout is given, but the summary function can later be
applied to a saved result to get