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haplo.stats (version 1.2.1)

Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

Description

Haplo Stats is a suite of S-PLUS/R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The genetic markers are assumed to be codominant (i.e., one-to-one correspondence between their genotypes and their phenotypes), and so we refer to the measurements of genetic markers as genotypes. The main functions in Haplo Stats are: haplo.em, haplo.glm and haplo.score.

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Install

install.packages('haplo.stats')

Monthly Downloads

1,656

Version

1.2.1

License

Copyright 2003 Mayo Foundation for Medical Education and Research. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. For other licensing arrangements, please contact Daniel J. Schaid, Ph.D., Division of Biostatistics, Harwick Building Room 775, Mayo Clinic, 200 First St., SW, Rochester, MN 55905. Phone: 507-284-0639, fax: 507-284-9542 email: schaid@mayo.edu

Maintainer

Jason Sinnwell

Last Published

September 20th, 2024

Functions in haplo.stats (1.2.1)

haplo.cc

Haplotype Association Analysis in a Case-Control design
haplo.scan.obs

For observed data, slide a fixed-width window over each marker locus and scan all possible haplotypes within the window
glm.fit.nowarn

Modified from glm.fit function to not warn users for binomial non-integer weights.
dglm.fit

Density function for GLM fit
Ginv

Compute Generalized Inverse of Input Matrix
haplo.hash

Integer Rank Codes for Haplotypes
haplo.score.glm

Compute haplotype score statistics for GLM
haplo.score.podds

Compute Haplotype Score Statistics for Ordinal Traits with Proportional Odds Model
haplo.glm

GLM Regression of Trait on Ambiguous Haplotypes
locus

Creates an object of class "locus"
hla.demo

HLA Loci and Serologic Response to Measles Vaccination.
haplo.em.control

Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.em

EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.model.frame

Sets up a model frame for haplo.glm
plot.haplo.score.slide

Plot a haplo.score.slide Object
print.haplo.score.slide

Print the contents of a haplo.score.slide object
mf.gindx

Model Frame Genotype Index to Account for Missing Data in haplo.glm
geno.recode

Recode Genotypes
haplo.score.merge

Merge haplo.score And haplo.group Objects
setupGeno

Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.
loci

Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.
summaryGeno

Summarize Full Haplotype Enumeration on Genotype Matrix
louis.info

Louis Information for haplo.glm
print.haplo.cc

Print a haplo.cc object
residScaledGlmFit

Scaled Residuals for GLM fit
haplo.score.slide

Score Statistics for Association of Traits with Haplotypes
na.geno.keep

Remove rows with NA in covariates, but keep genotypes with NAs
haplo.em.fitter

Compute engine for haplotype EM algorithm
print.haplo.em

Print contents of a haplo.em object
haplo.group

Frequencies for Haplotypes by Grouping Variable
summary.haplo.em

Summarize contents of a haplo.em object
plot.haplo.score

Plot Haplotype Frequencies versus Haplotype Score Statistics
printBanner

Print a nice banner
score.sim.control

Create the list of control parameters for simulations in haplo.score
print.haplo.score.merge

Print a haplo.score.merge object
allele.recode

Recode allele values to integer ranks
haplo.scan.sim

For simulated data, slide a fixed-width window over each marker locus and scan all possible haplotypes within the window
varfunc.glm.fit

Variance Function for GLM
haplo.enum

Enumerate all possible pairs of haplotypes that are consistent with a set of un-phased multilocus markers
haplo.chistat

Calculate a score test statistic for haplotypes
haplo.score

Score Statistics for Association of Traits with Haplotypes
print.haplo.glm

Print a contents of a haplo.glm object
print.haplo.group

Print a haplo.group object
setupData

Set up an example dataset provided within the library.
print.haplo.scan

Print a haplo.scan object
print.haplo.score

Print a haplo.score object
locator.haplo

Find Location from Mouse Clicks and Print Haplotypes on Plot
haplo.glm.control

Create list of control parameters for haplo.glm
geno.count.pairs

Counts of Total Haplotype Pairs Produced by Genotypes
haplo.scan

Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window