Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
Count the number of markers in the data
Initialization of the Rmpi cluster
Line-by-line modification of files
Count the number of families in the data
Count the number of individuals in the data
Closing the Rmpi cluster
Extracting part of genetic data.
Extract a part of an ff array (matrix) and return it as numeric matrix
Getter for the list with genetic or environmental data
Combine a sequence of files by columns
Convert large ped files by creating unique IDs, converting allele codi...
Checking uniqueness of individuals' IDs
Converting Haplin-formatted matrix into the new format
Create family matrix of data missingness
Intern function for creating column names for genotype data
Loading the data previously read in and saved by "genDataRead"
Pre-processing of the genetic data
Reading the genetic data from a file
Getter for all rows with children data
Getter only for all dyads (child and one parent)
Getter for all rows with fathers' data
Getter for all full triads
Getter for all rows with mothers' data
Test for gene-environment interaction
Fitting log-linear models to case-parent triad and/or case-control dat...
Run haplin analysis in a series of sliding windows over a sequence of ...
Fit haplin to each subset/stratum of data, determined by the argumen...
Power simulation for association analyses with Haplin
Asymptotic power calculations for genetic association analyses with Ha...
Relative efficiency comparing different study designs in genetic assoc...
Simulates genetic data and runs Haplin for each simulation
Simulation of genetic data in Haplin format
Create haplin table
Save files with summary, table, and plot from a haplin object.
Convert from ped format data to Haplin format
The Johnson distributions
Plot a haplin object
Plotter function for haplinSlide.
Print a haplin object
Plotter function for haplinStrat results.
Plot a haptable object
Plotting p-values for relative risks
QQ-plot with confidence intervals for a vector of p-values
Print the summary of a haplin object
Combine a sequence of files by rows
Display chosen genotypes
Display phenotype part of data
Display marker names
Find the column numbers of SNP identifiers/SNP numbers in a ped file
Power calculations for a single SNP
Sample size calculations for a single SNP
Compute a joint p-value for a list of haplin fits (usually from a slid...
Summary of a haplin object
Stack dataframes from haplinSlide into a single dataframe
Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in "Gjessing HK and Lie RT. Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes. Annals of Human Genetics (2006) 70, pp. 382-396".