SNPFastImpute-package: SNPFastImpute: Perform fast missing value imputation for...
In GaoGN517/689_SNP_FastImpute: SNPFastImpute: Perform fast missing value imputation for single nucleotide polymorphism data.
Description
Details
Author(s)
References
Description
The package performs single nucleotide polymorphism (SNP)
missing value imputation for their next generation gene
sequencing data without a reference genome. The tool should
be able to predict the missing SNP value based on a certain
number of SNPs around the missing point.
Details
Read in vcf file time or raw sequencing files, and impute missing single SNP values. This package currently containing a few
testing features that introduces additional missing positions to test different methods.
Main functions:
Impute_GenoType_XGBoost
Create_Single_SNP_Object
classfication_error
Generate_NA
vcf2df
Author(s)
Guannan Gao
Maintainer: Guannan Gao <gaog@stat.tamu.edu>
References
Kabisch, Maria, Ute Hamann, and Justo Lorenzo Bermejo. "Imputation of
missing genotypes within LD-blocks relying on the basic coalescent and
beyond: consideration of population growth and structure." BMC genomics 18.1 (2017): 798.
Tianqi Chen and Carlos Guestrin, "XGBoost: A Scalable Tree Boosting System",
22nd SIGKDD Conference on Knowledge Discovery and Data Mining, 2016, https://arxiv.org/abs/1603.02754
GaoGN517/689_SNP_FastImpute documentation built on Jan. 2, 2020, 11:44 a.m.
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Description Details Author(s) References
Description
The package performs single nucleotide polymorphism (SNP) missing value imputation for their next generation gene sequencing data without a reference genome. The tool should be able to predict the missing SNP value based on a certain number of SNPs around the missing point.
Details
Read in vcf file time or raw sequencing files, and impute missing single SNP values. This package currently containing a few testing features that introduces additional missing positions to test different methods.
Main functions:
Impute_GenoType_XGBoost
Create_Single_SNP_Object
classfication_error
Generate_NA
vcf2df
Author(s)
Guannan Gao
Maintainer: Guannan Gao <gaog@stat.tamu.edu>
References
Kabisch, Maria, Ute Hamann, and Justo Lorenzo Bermejo. "Imputation of missing genotypes within LD-blocks relying on the basic coalescent and beyond: consideration of population growth and structure." BMC genomics 18.1 (2017): 798.
Tianqi Chen and Carlos Guestrin, "XGBoost: A Scalable Tree Boosting System", 22nd SIGKDD Conference on Knowledge Discovery and Data Mining, 2016, https://arxiv.org/abs/1603.02754
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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