query_1000G: query_1000G.R

In ryanrsun/LungCancerAssoc: Pathway Analysis Using Summary Statistics

Description

Get 1000G subject SNPs at specific locations on the genome. This is a little less disk-space intensive than using 'wget' to download entire chromosome files. Only use for one region at a time (region is one contiguous block on one chromosome). NOTE: You must have the vcf_to_ped_covert.pl script (provided on 1000G website) in your working directory!

Usage

query_1000G(CHR, start_bp, end_bp, gene_name, buffer, pop_vec, Snum, aID,
  checkpoint = T)

Arguments

CHR	The chromosome where your region is located.
start_bp	The starting BP of the region.
end_bp	The ending BP of the region.
gene_name	Name of region you are querying, for error messages.
buffer	Add additional distance to the start and end of the region, possibly to capture nearby effects such as cis-eQTLs.
pop_vec	A vector containing strings describing the populations you want to query. See 1000G websites for the population codes.
Snum	Used in cluster job submission scripts to organize jobs. Must be numeric.
aID	Used in cluster job submission scripts to organize jobs. Must be numeric.
checkpoint	Would you like the function to print diagnostic/error messages?

Value

Return 0 for success and 1 for error.

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.