R package:blupADC-Feature 2

Overview

🤖 Generally, most genotype data need to perform quality control and imputation before applying in animal and plant breeding. For convenience, package blupADC provides genotype_data_QC_Imputation function to perform quality control and imputation by interfacing with software Plink and software Beagle in an easy way (we only need to provide the software path and software name).

👉 Note: For convenience, blupADC has encapsulated software Plink(for quality control) version-1.9 and software Beagle(for imputation) version-5.2. If you want change this version, you should set the related parameters in the part of Advanced parameter.

Example

library(blupADC)
geno_qc_impute(
            input_data_hmp=example_data_hmp,    #provided hapmap data object
            data_analysis_method="QC_Imputation",   #analysis method type,QC + imputatoin
            output_data_path=getwd(),               #output data path
            output_data_name="YY_data",             #output data name
            output_data_type="VCF"                  #output data format 
            )                       

In the process of quality control and imputation，we should provide genotype data，these parameters are the as in geno_format function(see more details).

Parameter

💙Basic

• 1：data_analysis_method

  Method of analyzing data, character class.

  • "QC" : only perform quality control
  • "Imputation" : only perform imputation

• "QC_Imputation" : first perform quality control, and then perform imputation

• 2：qc_snp_rate

Threshold of SNPs call rate in quality control, numeric class. Default is 0.1

• 3：qc_ind_rate

Threshold of individuals call rate in quality control, numeric class. Default is 0.1

• 4：qc_maf

Threshold of minor allele frequency(MAF) in quality control, numeric class. Default is 0.05

• 5：qc_hwe

Threshold of hardy weinberg equilibrium(HWE) in quality control, numeric class. Default is 1e-7

💜Advanced

• 6：plink_software_path

Path of software Plink , character class.

• 7：plink_software_name

Name of software Plink , character class.

• 8：beagle_software_path

Path of software Beagle , character class.

• 9：beagle_software_name

Name of software Beagle , character class.

• 10：beagle_ref_data_path

File path of reference data in imputation, character class.

• 11：beagle_ref_data_name

File name of reference data in imputation, character class.

• 12：beagle_ped_path

File path of pedigree data in imputation, character class.

• 13：beagle_ped_name

File name of pedigree data in imputation, character class.