clean_1000G_raw: clean_1000G_raw.R

In ryanrsun/LungCancerAssoc: Pathway Analysis Using Summary Statistics

Description

After querying data from 1000G, clean the raw data (mostly remove non-biallelic SNPs).

Usage

clean_1000G_raw(fname_root, gene_name, start_bp, end_bp, checkpoint)

Arguments

fname_root	The root (everything before .ped) of the downloaded 1000G file.
gene_name	A name (often a gene name, but not always) for the region of SNPs you have downloaded, only to print with error messages.
start_bp	The starting position of the range we want.
end_bp	The ending position of the range we want.
checkpoint	A boolean, if TRUE, print out diagnostic/error messages.

Value

A list with the elements info_file and ped_file, containing the (clean) genotype info and counts.

Examples

query_1000G(CHR=1, start_bp=100000, end_bp=200000, buffer=10000, pop_vec='GBR')

ryanrsun/LungCancerAssoc documentation built on May 24, 2019, 7:26 p.m.