Create_SNP_XGBoost_Object: Input a dataframe, generate an object for the SNP missing...

In GaoGN517/689_SNP_FastImpute: SNPFastImpute: Perform fast missing value imputation for single nucleotide polymorphism data.

Description

Input a dataframe, generate an object for the SNP missing value imputation with xgboost.

Usage

Create_SNP_XGBoost_Object(df, size = 10)

Arguments

df	A dataframe of the SNPs which we need to impute missing values
size	A windows size which we control for our imputation. Default value is 50.

Details

This function takes in a matrix (p columns of SNPs, n rows of samples) with NAs and returns an object for our imputation function.

Value

a list of list of 2 contents:

1. NA_cols: column index with missing values

2. Multiple_SNP_Object: corresponding SNP_Objects for these SNPs

Examples

## This is a short matrix containing 100 SNPs with 20 samples. 
data("Test_df")
xgboost_snp_obj <- Create_SNP_XGBoost_Object(df)

xgboost_snp_obj <- Create_SNP_XGBoost_Object(df, size = 200)

GaoGN517/689_SNP_FastImpute documentation built on Jan. 2, 2020, 11:44 a.m.