aba.query: aba.query() - Query aba results for all positive results

In tobyjohnson/gtx: Genetics ToolboX

Description

Query all colocalization data in a region or set of traits. Typical use is to query a gene ID (ensemblid or hgncid) and to pull all coloc data in the surrounding queried region (+/- surround bp). A region can also be specified using: chrom, pos_start, & pos_end. Alternatively, a set of traits can be queried instead of the entire aba to help generate hypothesis before looking at specific loci. The aba.query() will return only positive results based on filtering (using params below).

Usage

aba.query(analysis_ids, hgncid, ensemblid, rsid, chrom, pos, pos_start,
  pos_end, p12_ge = 0.8, minpval1_le = 1e-04, minpval2_le = 5e-08,
  surround = 1e+06, ncase_ge = 200, ncohort_ge = 200,
  protein_coding_only = FALSE, neale_only = FALSE, gsk_only = FALSE,
  ttam_only = FALSE, db = gtx::config_db(),
  impala = getOption("gtx.impala", NULL))

Arguments

analysis_ids	ukbiobank analysis id(s), single string or vector.
hgncid	HGNC symbol. Single string or vector.
ensemblid	Ensembl gene ID. Single string or vector.
rsid	SNP rsid. Single string or vector.
chrom	chromosome - Used to define a specific region
pos	position that will have +/- surround for bounds to pull in colocs.
pos_start	start position - Used to define a specific region, overrides surround
pos_end	end position - Used to define a specific region, overrides surround
p12_ge	[Default >= 0.80] This is the "H4" posterior probability cutoff
minpval1_le	[Default <= 1e-4] Min pval seen in the eQTL
minpval2_le	[Default <= 5e-8] Min pval seen in the GWAS data
surround	[Default = 1e6] Distance to pull in TH + respective genes.
ncase_ge	[Default >= 200] Minimum ncases for traits.
ncohort_ge	[Default >= 200] Minimum ncohort for traits.
protein_coding_only	[Default = FALSE] Filter only for protein coding transcripts
neale_only	[Default = FALSE] Filter only for Neale traits, reduces redundancy b/w GSK & Neale data.
gsk_only	[Default = FALSE] Filter only for GSK traits, reduces redundancy b/w GSK & Neale data.
ttam_only	[Default = FALSE] Filter only for 23andMe (TTAM) traits.
db	[Defalt = gtx::config_db()] Database to pull data from.
impala	[getOption("gtx.impala", NULL)] Implyr impala connection

Value

data.frame with all coloc results in the region

Author(s)

Karsten Sieber [e-mail]

Examples

Query aba colocs:
colocs <- aba.query(hgncid = "HMGCR")

colocs <- aba.query(analysis_ids = "ukb_cool_analysis_id")

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.