deletion: deletion searching

Description Usage Arguments Value Author(s)

Description

function of searching for the next grouping given deleted SNPs

Usage

1
deletion(lib, lib.names, case.sub, ctl.sub, aic.now, dev.now, df.now, rank = FALSE, cut = -1, delete.snp = -1, ref = "NA", alpha = 0.05, step = 0)

Arguments

lib

the alleles library contains allele sequences for those only appear in the case and control samples

lib.names

the corresponding names of the alleles

case.sub

case subjects, two columns for two haplotypes

ctl.sub

control subjects, two columns for two haplotypes

aic.now

aic for the current model

dev.now

deviance for the current model

df.now

degree of freedom for the current model

rank

numbers of pairs with top similarity scores to be investigate if FALSE, then deviance is calculated for the step-wise merger, then option "alpha" and "step" is used

cut

cutoff for similarity score to be consider, default is -1, means all scores above 0

delete.snp

a vector of position of deleted SNPs

ref

allele names for the reference level, the default reference level (ref="NA") is the most common allelels

alpha

family-wise error, used for deviance only

step

index for how many deletions have been carried so far

Value

del

position of deleted SNPs

aic

AIC

df

degree of freedom

dev

deviance

stop

1: no merge found

record

the record of the searching path

Author(s)

Xin Huang


HAP.ROR documentation built on May 1, 2019, 10:24 p.m.