Description Usage Format Details Examples
A table of information about the 10 SNPs in dataset geno
, in a format reminiscent of a PLINK binary map (.bim) file.
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A data frame with 10 rows, 1 per SNP. There are 6 labeled columns, for the following variables:
chr
Chromosome numbers
SNP
A vector of SNP rs numbers, as character strings.
position
SNP position, in base-pairs, from HapMap Build 36.
Ref_Allele
Vector of reference alleles, as character strings, from the HapMap positive strand. Genotypes on each SNP in dataset geno
are counts of its reference allele.
Other_Allele
The "other allele." Also a vector of character strings.
Freq_Ref_Allele
The relative frequency of the reference allele, in HapMap CEU reference data.
See documentation for dataset geno
for details on how the genotypic data on these SNPs was simulated. See documentation for dataset pheno
for details on how the effect locus, rs7681769, was used to simulate phenotypic data.
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Loading required package: bdsmatrix
Attaching package: 'bdsmatrix'
The following object is masked from 'package:base':
backsolve
Loading required package: Matrix
'data.frame': 10 obs. of 6 variables:
$ chr : int 1 2 3 4 5 6 7 8 9 10
$ SNP : chr "rs3934834" "rs2204204" "rs12493026" "rs7681769" ...
$ position : int 995669 45759450 82695340 190468410 145620180 86687095 33251263 12924148 683182 116070
$ Ref_Allele : chr "C" "T" "C" "C" ...
$ Other_Allele : chr "T" "C" "T" "A" ...
$ Freq_Ref_Allele: num 0.88 0.82 0.93 0.43 0.74 0.72 0.88 0.2 0.79 0.89
chr SNP position Ref_Allele Other_Allele Freq_Ref_Allele
1 1 rs3934834 995669 C T 0.88
2 2 rs2204204 45759450 T C 0.82
3 3 rs12493026 82695340 C T 0.93
4 4 rs7681769 190468410 C A 0.43
5 5 rs2304033 145620180 A G 0.74
6 6 rs10944161 86687095 A C 0.72
7 7 rs6952877 33251263 T G 0.88
8 8 rs475181 12924148 C A 0.20
9 9 rs17432514 683182 T C 0.79
10 10 rs11591988 116070 C T 0.89
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