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Haplin (version 7.3.1)

Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes

Description

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".

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Version

Install

install.packages('Haplin')

Monthly Downloads

278

Version

7.3.1

License

GPL (>= 2)

Maintainer

Hakon Gjessing

Last Published

February 8th, 2024

Functions in Haplin (7.3.1)

hapRun

Simulates genetic data and runs Haplin for each simulation
initParallelRun

Initialization of the Rmpi cluster
output

Save files with summary, table, and plot from a haplin object.
haplinSlide

Run haplin analysis in a series of sliding windows over a sequence of markers/SNPs
nsnps

Count the number of markers in the data
haplin

Fitting log-linear models to case-parent triad and/or case-control data
plot.haplinSlide

Plotter function for haplinSlide.
lineByLine

Line-by-line modification of files
haplinStrat

Fit haplin to each subset/stratum of data, determined by the argument strata
nfam

Count the number of families in the data
pQQ

QQ-plot with confidence intervals for a vector of p-values
pJohnson

The Johnson distributions
haptable

Create haplin table
getChildren

Getter for all rows with children data
hapSim

Simulation of genetic data in Haplin format
plot.haplinStrat

Plotter function for haplinStrat results.
hapPowerAsymp

Asymptotic power calculations for genetic association analyses with Haplin
nindiv

Count the number of individuals in the data
print.summary.haplin

Print the summary of a haplin object
plot.haplin

Plot a haplin object
plot.haptable

Plot a haptable object
pedToHaplin

Convert from ped format data to Haplin format
print.haplin

Print a haplin object
hapRelEff

Relative efficiency comparing different study designs in genetic association analysis with Haplin
showPheno

Display phenotype part of data
plotPValues

Plotting p-values for relative risks
rbindFiles

Combine a sequence of files by rows
snpPower

Power calculations for a single SNP
snpPos

Find the column numbers of SNP identifiers/SNP numbers in a ped file
showSNPnames

Display marker names
snpSampleSize

Sample size calculations for a single SNP
suest

Compute a joint p-value for a list of haplin fits (usually from a sliding window approach), correcting for multiple testing.
summary.haplin

Summary of a haplin object
toDataFrame

Stack dataframes from haplinSlide into a single dataframe
showGen

Display chosen genotypes
cbindFiles

Combine a sequence of files by columns
genDataGetPart

Extracting part of genetic data.
f.create.snp.names

Intern function for creating column names for genotype data
finishParallelRun

Closing the Rmpi cluster
getFullTriads

Getter for all full triads
genDataLoad

Loading the data previously read in and saved by "genDataRead"
getFathers

Getter for all rows with fathers' data
genDataRead

Reading the genetic data from a file
genDataPreprocess

Pre-processing of the genetic data
getMothers

Getter for all rows with mothers' data
gxe

Test for gene-environment interaction
create.missingness.matrix

Create family matrix of data missingness
f.check.unique.ids

Checking uniqueness of individuals' IDs
f.extract.ff.numeric

Extract a part of an ff array (matrix) and return it as numeric matrix
f.get.gen.data.cols

Getter for the list with genetic or environmental data
f.convert.matrix.ff

Converting Haplin-formatted matrix into the new format
convertPed

Convert large ped files by creating unique IDs, converting allele coding and extracting a selection of SNPs
getDyads

Getter only for all dyads (child and one parent)
hapPower

Power simulation for association analyses with Haplin