genotype: Example genotype data

In reGenotyper: Detecting Mislabeled Samples in Genetic Data

Description

genotype: example data of genotype for each marker (rownames) and 60 strains such as recombinant inbred lines (RIL) (columnnames), with numeric values 1 and 0 (or A and B). In total there are 5 chromosomes with 20cM in length for each chromosome. In each chromosome, 20 markers are evenly distributed on each chromosome. As an example, 10 percent (=6) samples were added as mislabeled sample by swapping.

data(genotype)
genotype[1:5,1:5]

	Sample1	Sample2	Sample3	Sample4	Sample5
C1M1	1	0	0	1	0
C1M2	1	0	0	1	0
C1M3	1	0	0	1	0
C1M4	1	0	0	1	0
C1M5	1	0	0	1	0

Usage

data(genotype)

Format

genotype: 120 markers by 100 samples.

Author(s)

Yang Li <[e-mail]>

Examples

  ##load the data
  data(genotype)
  
  ##view part of the the data
  genotype[1:5,1:5]

Example output

Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: MatrixEQTL
     Strain1 Strain2 Strain3 Strain4 Strain5
D1M1       0       1       0       0       0
D1M2       0       1       0       0       0
D1M3       0       1       0       0       0
D1M4       0       1       0       0       0
D1M5       0       1       0       0       0

reGenotyper documentation built on May 1, 2019, 11:08 p.m.