get.snps.bbmri: Get SNP data (BBMRI)

Description Usage Arguments Examples

Description

This function transforms SNP data (virtual machine): limits analysis to specified biobanks, reads in genotype data in chunks, removes SNPs with missing values (multiple biobanks/technologies), removes SNPs with low minor allele frequency, fuses data from multiple biobanks/technologies

Usage

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get.snps.bbmri(chr, biobank = NULL, path = getwd(), size = 500 *
  10^3)

Arguments

chr

chromosome: integer 1-22

biobank

character "CODAM", "LL", "LLS", "NTR", "PAN", "RS", or NULL (all)

path

data directory

size

maximum number of SNPs to read in at once; trade-off between memory usage (low) and speed (high)

Examples

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path <- "/virdir/Scratch/arauschenberger/trial"

rauschenberger/spliceQTL documentation built on May 13, 2019, 3:02 a.m.