haplinTDT, which is the result of
Transmission disequilibrium tests of data.
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)filename is required. Use of the remaining arguments will depend on the type of analysis. haplinTDT does not do
a permutation test.haplin using the EM
algorithm.
The haplotypes are then
analysed as a single multiallelic marker. If use.haplotypes=FALSE,
the markers are analysed individually.haplinTDT uses all
available markers in the data set in the analysis. If
use.haplotypes = TRUE then for the current
version of haplin the number of markers used at a single run
should probably not exceed 4 or 5 due to the computational
burden. The markers argument can be used to select appropriate
markers from the file without creating a new file for the selected
markers. For instance, if markers is set to c(2,4), haplinTDT will
only use the second and fourth markers supplied in the data
set. When running haplinTDT, it may be a good idea to start
exploring a few markers at a time, using this argument. haplinTDT uses haplin to reconstruct the markers or haplotypes. The default, however, is
FALSE. When FALSE, all triads having any sort of missing data are
excluded before the analysis is run. Note that haplinTDT only looks at
markers actually used in the analysis, so that if the markers
argument (see below) is used to select a collection of markers for
analysis, haplinTDT only excludes triads with missing data on the
included markers.haplinTDT assumes the markers are on the x-chromosome. This option
should be combined with specifying the sex argument.xchrom = TRUE.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 the same summary.haplinTDT is returned
Let t_ij be the number of parents transmitting
allele i and not j to its child and let n be number of alleles. The
standard TDT test is then defined as
the sum of terms (t_ij - t_ji)^2/(t_ij + t_ji) for 1<=i The Triad Multi-Marker test (TRIMM) test is only defined for
diallelic markers. If use.ambiguous = FALSE, then all ambiguous trios will be removed.
Otherwise, the different contributions
to TDT, HHRR and TRIMM are weighted with the probabilities of the
different transmission configurations of alleles from parent to child. For example if the
parents and the child are all heterozygous 1/2, then with probability
0.5 the mother (or father) will transfer allele 1 and not allele 2.
The standard formulation of the TDT and HHRR tests
correspond to having use.ambiguous = TRUE.
Transmission disequilibrium test (TDT): Spielman RS, McGinnis RE and Ewens WJ. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). American Journal of Human Genetics (1993) 52(3), pp. 506-16.
Triad multi-marker test (TRIMM): Shi M, Umbach DM and Weinberg CR. Identification of risk-related haplotypes with the use of multiple SNPs from nuclear families. The American Journal of Human Genetics (2007) 81, pp. 53-66.
summary.haplinTDT, plot.haplinTDT
## Not run:
#
# # Standard run with permutation test:
# res <- haplinTDT("data.dat", nsim.perm=1000)
# # Plot the saved result:
# plot(res)
# # A full summary of saved result including p-values
# summary(res)
#
# # Include missing values:
# res <- haplinTDT("data.dat", nsim.perm=1000, use.missing=TRUE)
# ## End(Not run)
Run the code above in your browser using DataLab