/usr/lib/R/site-library/haplo.stats/INDEX is in r-cran-haplo.stats 1.4.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 | Ginv Compute Generalized Inverse of Input Matrix
chisq.power Power and sample size for the chi-square
distribution
f.power Power and sample size for the F distribution
find.haplo.beta.qt Find beta's for risk haplotypes, for specified
r2
geno.count.pairs Counts of Total Haplotype Pairs Produced by
Genotypes
geno.recode Internal functions for the HaploStats package
geno1to2 convert genotype matrix from 1-column 2-column
get.hapPair Get a list of objects for haplotype pairs
glm.fit.nowarn Modified from glm.fit function to not warn
users for binomial non-integer weights.
haplo.cc Haplotype Association Analysis in a
Case-Control design
haplo.design Build a design matrix for haplotypes
haplo.em EM Computation of Haplotype Probabilities, with
Progressive Insertion of Loci
haplo.em.control Create the Control Parameters for the EM
Computation of Haplotype Probabilities, with
Progressive Insertion of Loci
haplo.em.fitter Compute engine for haplotype EM algorithm
haplo.glm GLM Regression of Trait on Ambiguous Haplotypes
haplo.glm.control Create list of control parameters for haplo.glm
haplo.group Frequencies for Haplotypes by Grouping Variable
haplo.hash Integer Rank Codes for Haplotypes
haplo.model.frame Sets up a model frame for haplo.glm
haplo.power.cc Compute either power or sample size for
haplotype associations in a case-control study.
haplo.power.qt Compute either power or sample size for
haplotype associations with a quantitative
trait.
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
haplo.score Score Statistics for Association of Traits with
Haplotypes
haplo.score.merge Merge haplo.score And haplo.group Objects
haplo.score.slide Score Statistics for Association of Traits with
Haplotypes
hla.demo HLA Loci and Serologic Response to Measles
Vaccination.
locator.haplo Find Location from Mouse Clicks and Print
Haplotypes on Plot
loci Create a group of locus objects from a genotype
matrix, assign to 'model.matrix' class.
locus Creates an object of class "locus"
louis.info Louis Information for haplo.glm
na.geno.keep Remove rows with NA in covariates, but keep
genotypes with NAs
plot.haplo.score Plot Haplotype Frequencies versus Haplotype
Score Statistics
plot.haplo.score.slide
Plot a haplo.score.slide Object
plot.seqhap Plot a seqhap object
print.haplo.cc Print a haplo.cc object
print.haplo.em Print contents of a haplo.em object
print.haplo.glm Print a contents of a haplo.glm object
print.haplo.group Print a haplo.group object
print.haplo.scan Print a haplo.scan object
print.haplo.score Print a haplo.score object
print.haplo.score.merge
Print a haplo.score.merge object
print.haplo.score.slide
Print the contents of a haplo.score.slide
object
print.seqhap Print Contents of a Seqhap Object
printBanner Print a nice banner
score.sim.control Create the list of control parameters for
simulations in haplo.score
seqhap Sequential Haplotype Scan Association Analysis
for Case-Control Data
seqhap.dat Simulated data for seqhap examples
setupData Set up an example dataset provided within the
library.
setupGeno Create a group of locus objects from a genotype
matrix, assign to 'model.matrix' class.
summary.haplo.em Summarize contents of a haplo.em object
summaryGeno Summarize Full Haplotype Enumeration on
Genotype Matrix
x.sexcheck consistency checks for x.linked locus
|