R package:blupADC-Feature 3

Overview

👦 Breed composition analysis is usually a problem in data analysis. In package:blupADC, user can solve this problem by applying geno_check function. In addition, user can detect the duplication of genomic data easily by applying geno_check function.

Example

Breed composition analysis

library(blupADC)
check_result=geno_check(
                  input_data_hmp=example_PCA_data_hmp,   #provided hapmap data object
                  duplication_check=FALSE,       #whether check the duplication of genotype
                  breed_check=TRUE,              # whether check the record of breed
                  breed_record=example_PCA_Breed,        # provided breed record
                  return_result=TRUE             #return result 
                  )

Check duplication

library(blupADC)
check_result=geno_check(
                  input_data_hmp=example_data_hmp,   #provided hapmap data object
                 duplication_threshold=0.95, #threshold of duplication
                  duplication_check=TRUE,    #whether check the duplication of genotype
                  breed_check=FALSE,         # whether check the record of breed
                  return_result=TRUE         #return result 
                  )

Output

The result of output mainly contains two parts, including:

• duplicated_genotype

The first and the second column is the name of individual, the third column is the percentage of overlap.

• pca_outlier

Figure A is the PCA result before correcting breed record , Figure B is the PCA result after correcting breed correcting record

Parameter

Many parameters in genotype_data_overlap are the same as in genotype_data_format_conversion function (see more details).

Thus, we will introduce specific parameters in genotype_data_overlap function.

• 1：selected_snps

Number of SNPs in detecting overlap, numeric class. Default is 1000.

• 2：overlap_threshold

Threshold of duplicate genotype, numeric class. Default is 0.95.

• 3：duplication_check

Whether check duplication of genotype, logical class. Default is TRUE.

• 4：breed_check

Whether check breed record of genotype, logical class. Default is FALSE.

• 5：ind_breed

Breed record of individuals, data.frame class.

The format of ind_breed is showing as follow:

When the proportion of genotype data between two individuals is larger than this threshold, these two individuals will be regarded as the same individual.