myqc: Select genotype variables by Annovar

In jiayouzytx/StatComp21056: Select gene variables by Annovar

Description

The genotype data has high dimension, so it is difficult to analysis by many methods. Thus We can have a preliminary screening by ANNOVAR. ANNOVAR is a good way to handle with the SNP data, so we can apply the ideas to R. Firstly, import the exonic variant function by gene based annotation and Score alignment library, PolyPhen2, cadd, sift. The three scores can assess the importance of genes well. When there are two scores show that the gene is important, then keep it.

Usage

myqc(df, df2, pp2, cadd, sift)

Arguments

df	the exonic variant function by gene based annotation
df2	the other exonic variant function by gene based annotation
pp2	the database of PolyPhen2 scores
cadd	the database of cadd scores
sift	the database of sift scores

Value

a vector of important gene variables Allrs

Examples

## Not run: 
index<-myqc(df,df2,pp2,cadd,sift)

## End(Not run)

jiayouzytx/StatComp21056 documentation built on Dec. 23, 2021, 11:15 p.m.