index_regions: Get gene and SNP index for each region

In simingz/ctwas: Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits

Get gene and SNP index for each region

Description

For each region, get the index for snp and gene (index is location/column number in .pgen file or .expr file) located within this region.

Usage

index_regions(
  regionfile,
  exprvarfs,
  pvarfs = NULL,
  ld_Rfs = NULL,
  select = NULL,
  thin = 1,
  maxSNP = Inf,
  minvar = 1,
  merge = T,
  outname = NULL,
  outputdir = getwd()
)

Arguments

regionfile	regions file. Has three columns: chr, start, end. The regions file should provide non overlaping regions defining LD blocks. currently does not support chromsome X/Y etc.
select	Default is NULL, all variants will be selected. Or a vector of variant IDs, or a data frame with columns id and z (id is for gene or SNP id, z is for z scores). z will be used for remove SNPs if the total number of SNPs exceeds limit. See parameter 'maxSNP' for more information.
thin	A scalar in (0,1]. The proportion of SNPs left after down sampling. Only applied on SNPs after selecting variants.
maxSNP	Default is Inf, no limit for the maximum number of SNPs in a region. Or an integer indicating the maximum number of SNPs allowed in a region. This parameter is useful when a region contains many SNPs and you don't have enough memory to run the program. In this case, you can put a limit on the number of SNPs in the region. If z scores are given in the parameter 'select', i.e. a data frame with columns id and z is provided, SNPs are ranked based on |z| from high to low and only the top 'maxSNP' SNPs are kept. If only variant ids are provided, then 'maxSNP' number of SNPs will be chosen randomly.
minvar	minimum number of variatns in a region
merge	TRUE/FALSE. If TRUE, merge regions when a gene spans a region boundary (i.e. belongs to multiple regions.)
outname	a string, the output name
outputdir	a string, the directory to store output

Value

A list. Items correspond to each pvarf/exprvarf. Each Item is also a list, the items in this list are for each region.

simingz/ctwas documentation built on Sept. 17, 2024, 10:55 p.m.