map2bf.file: Calibrate a variant map from a file to Bayes Factors

In jweile/maveclin: Clinical predictions for MaveDB

Description

Calibrate a variant map from a file to Bayes Factors

Usage

map2bf.file(csvfile, ensembls, symbols, drawPlot = TRUE, minMaf = 0,
  flip = FALSE, homozygous = FALSE, overrideCache = FALSE,
  logger = NULL)

Arguments

csvfile	the scoreset file in csv format
ensembls	a vector of ensembl IDs for the target gene
symbols	a vector of gene symbols of the target gene
drawPlot	boolean value indicating whether a plot of variant distributions should be drawn. Defaults to TRUE.
minMaf	the minimum Minor Allele Frequency required for variants to be considered benign
flip	logical; whether to apply the flip transformation to the scores
homozygous	logical; filter benign variants to only those occuring homozygously.
overrideCache	logical; whether to override local cache.
logger	a yogilogger object to which to write log messages.

Value

a data.frame containing the original scores input with an additional column llr, representing the log likelihood ratio (i.e. log Bayes Factor)

jweile/maveclin documentation built on May 4, 2019, 3:08 a.m.