getSnpWeights: Extract p-value weights from a GWAS resultfile

In boostSeq: Optimized GWAS cohort subset selection for resequencing studies

Description

This is a very simple function that extracts for a number of SNPs their p-value from an association result file, e.g. generated by PLINK.

Usage

getSnpWeights(
  snps, 
  gwas.resultfile, 
  pColname = "P", 
  snpColname = "SNP"
) 

Arguments

snps	character. A vector of SNP identifiers for that p-values are extracted from gwas.resultfile.
gwas.resultfile	character. Path/filename to the file containing SNPs and p-values. Has to contain a column header line and be readable by the read.table function.
pColname	character. Name of the column containing p-values.
snpColname	character. Name of the column containing SNP identifiers.

Value

A vector containing wheights which are 1 plus the difference to the smallest log P among all SNPs requested. Names of the elements are the according SNP IDs.

Examples

## path to example data
gwas.resultfile <- system.file("extdata", "example.gwas", package = "boostSeq")

getSnpWeights(snps = c("rs8411", "rs7960808"), gwas.resultfile)  

Example output

Loading required package: genetics
Loading required package: combinat

Attaching package: 'combinat'

The following object is masked from 'package:utils':

    combn

Loading required package: gdata
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to locate valid perl interpreter
gdata: 
gdata: read.xls() will be unable to read Excel XLS and XLSX files
gdata: unless the 'perl=' argument is used to specify the location of a
gdata: valid perl intrpreter.
gdata: 
gdata: (To avoid display of this message in the future, please ensure
gdata: perl is installed and available on the executable search path.)
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith

Loading required package: gtools
Loading required package: MASS
Loading required package: mvtnorm


NOTE: THIS PACKAGE IS NOW OBSOLETE.



  The R-Genetics project has developed an set of enhanced genetics

  packages to replace 'genetics'. Please visit the project homepage

  at http://rgenetics.org for informtion.




Attaching package: 'genetics'

The following objects are masked from 'package:base':

    %in%, as.factor, order

Loading required package: lpSolveAPI
rs7960808    rs8411 
 1.000000  1.485491 

boostSeq documentation built on May 30, 2017, 5:47 a.m.