Read data from different input files

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Description

Data can be loaded in different formats.

Usage

1
read.data(filename, linkage = TRUE, map = NA)

Arguments

filename

the name of the file which the data are to be read from.

linkage

a logical value indicating whether the file is in linkage format.

map

Localizion of a map file.

Details

1) single individuals (3-columns)
expected columns
Individual identifier
genotype STRING (1=homozygot (wildtype) 2=homozygot (variant) 3=heterozygote 0=missing value) >> Example: "1223" "3023"
phenotype

2) family data (4-columns)
expected columns
Family identifier
Individual identifier
genotype (1=homozygot (wildtype) 2=homozygot (variant) 3=heterozygote 0=missing value) >> Example: "1223" "3023"
phenotype
Remark 1: patid should not be 0 because 0 is unkown value for fid and mid.
Remark 2: Families are sorted. First two person in a family are adults (father and then mother) and after that all children.

3) Linkage format is expected, if linkage=TRUE :
Family identifier
Individual identifier
Father identifier (0=unkown)
Mother identifier (0=unkown)
Sex (0=unkown,1=male,2=female)
Affectation_status (0=unkown,1=unaffected,2=affected) or trait_value
Marker_genotypes (M1_A1 M1_A2 M2_A1 ...) >> only 1, 2, or 0 for missing values

4) map file (4-columns), if specified:
chromosome (1-22, only autosomes)
snp identifier
Genetic distance (morgans)
Base-pair position (bp units)

Value

famid

family identifier

patid

individual identifier

fid

father identifier (0=unkown)

mid

mother identifier (0=unkown)

sex

sex (0=unkown,1=male,2=female)

genotypes

(n,m)-matrix; n=No. of individuals; m=No. of SNPs; Klaus format

trait

phenotype values

chr

chromosome

snp

snp identifier or rs id

pos

Base-pair position on chromosome (base pair units)

Author(s)

Sven Knueppel