/usr/lib/R/site-library/genetics/NAMESPACE is in r-cran-genetics 1.3.8.1-1.
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 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 | import(MASS, combinat)
export(
HWE.chisq,
HWE.exact,
HWE.test,
LD,
#binsearch, # moved to gtools
ci.balance,
diseq,
diseq.ci,
genotype,
haplotype,
is.genotype,
is.haplotype,
as.genotype,
as.haplotype,
allele.names,
nallele,
gregorius,
homozygote,
heterozygote,
carrier,
allele,
allele.count,
allele.names,
#library.pos,
locus,
gene,
marker,
"locus<-",
"gene<-",
"marker<-",
is.gene,
is.locus,
is.marker,
getlocus,
getmarker,
getgene,
makeGenotypes,
makeHaplotypes,
power.casectrl,
LDtable,
LDplot,
as.factor,
geno.as.array,
# mknum,
hap,
hapshuffle,
hapenum,
hapfreq,
hapmcmc,
mourant,
hapambig,
write.pop.file,
write.pedigree.file,
write.marker.file,
shortsummary.genotype,
summary.LD.data.frame,
as.genotype.allele.count,
expectedGenotypes,
expectedHaplotypes,
order,
genotypeOrder,
"genotypeOrder<-",
groupGenotype,
"%in%"
)
S3method(summary,genotype)
#S3method(allele.count.2,genotype)
#S3method(as.factor.allele,genotype)
S3method(as.factor,default)
S3method(as.factor,genotype)
#S3method('<-',locus)
#S3method('<-',marker)
#S3method('<-',gene)
S3method(print,gene)
S3method(print,locus)
S3method(print,marker)
S3method(as.character,locus)
S3method(as.character,gene)
S3method(as.character,marker)
S3method(carrier,genotype)
S3method(as.genotype,allele.count)
S3method(as.genotype,character)
S3method(as.genotype,default)
S3method(as.genotype,factor)
S3method(as.genotype,genotype)
S3method(as.genotype,haplotype)
S3method(as.genotype,table)
S3method(HWE.chisq,genotype)
S3method(HWE.test,genotype)
S3method(HWE.test,data.frame)
S3method(print,HWE.test)
S3method(LD,genotype)
S3method(LD,data.frame)
S3method(diseq,table)
S3method(diseq,genotype)
S3method(print,diseq)
S3method(print,genotype)
S3method('==',genotype)
S3method('==',haplotype)
S3method('%in%',default)
S3method('%in%',genotype)
S3method('%in%',haplotype)
S3method('[',genotype)
S3method('[',haplotype)
S3method('[<-',genotype)
S3method('[<-',haplotype)
S3method(heterozygote,genotype)
S3method(homozygote,genotype)
#S3method(print,allele.count)
S3method(print,allele.genotype)
#S3method(allele.count,genotype)
#S3method(allele,genotype)
S3method(print,LD)
S3method(print,LD.data.frame)
S3method(print,summary.LD.data.frame)
S3method(plot,LD.data.frame)
S3method(print,summary.genotype)
S3method(plot,genotype)
S3method(order, default)
S3method(order, genotype)
S3method(sort, genotype)
importFrom(stats, na.omit)
importFrom(gdata, interleave, trim)
importFrom(mvtnorm, rmvnorm)
##importFrom(combinat, rmultz2) # combinat doesn't have a namesspace.
importFrom(gtools, binsearch, combinations, permutations)
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