as.GWAS: Create a GWAS object

In aaronwolen/bingd: Bayesian integration of genomic data

Description

Create a GWAS object from a data.frame or a GRanges object.

Usage

as.GWAS(object, genome, marker, chr, bp, pvalue, zscore, or, beta)

## S4 method for signature 'data.frame'
as.GWAS(object, genome, marker, chr, bp, pvalue, zscore,
  or, beta)

## S4 method for signature 'GRanges'
as.GWAS(object, genome, marker, pvalue, zscore, or, beta)

Arguments

object	a data.frame or GRanges object containing the required fields necessary to construct a GWAS object
genome	genome abbreviation used by UCSC (e.g., hg19)
marker	name of the column in object that contains the marker (or SNP) identifiers
chr	name of the column in object that contains the chromosome names associated with each marker
bp	name of the column in object that contains the genomic position (or start position) associated with each marker
pvalue	name of the column in object that contains the GWAS association p-value for each marker
zscore	name of the column in object that contains the GWAS z-scores for each marker
or	name of the column in object that contains the GWAS odds ratio for each marker
beta	name of the column in object that contains the GWAS beta values (or regression coefficients) for each marker

Methods (by class)

• data.frame: Create a GWAS object from a data.frame

• GRanges: Create a GWAS object from a GRanges object

aaronwolen/bingd documentation built on May 10, 2019, 4:04 a.m.