map: SNP "map" file
In RFGLS: Rapid Feasible Generalized Least Squares

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.

data(map)

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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data(map)
str(map)
map

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