shapeit_set_ancestor: Adjust Ancentral/Derived Alleles According to Reference

Description Usage Arguments Details Value Author(s) Examples

View source: R/shapeit_set_ancestor.R

Description

Adjust Ancentral/Derived Alleles According to Reference

Usage

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shapeit_set_ancestor(
  shapeit,
 
    ref = "~/cmcouto.silva@usp.br/lab_files/datasets/Reference_annotation/1000g_ancestor/human_ancestor_GRCh37_e59/",
  out
)

Arguments

shapeit

Scalar character with the name of the dataset file on Shapeit format without extension (.haps/.sample).

ref

Scalar character with the path of the reference fasta files (1000G).

out

Scalar character with desired name for the output file (without extension).

Details

Freely download of 1000 Genomes Ancestor alleles available at: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/

Value

Dataset with adjusted ancestral/derived alleles (.haps and .sample files).

Author(s)

CainĂ£ Max Couto-Silva

Examples

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## Not run: 
haps <- "dataset/my_phased_dataset"
ref <- "path_to_fasta_files/"
out <- "out_folder/phased_data_with_fixed_ancestor"

set_anc_alleles(sfile, ref, out)

## End(Not run)

cmcouto-silva/gt documentation built on June 6, 2021, 7:14 p.m.