preprocess_genedata

Preprocess genotype files in PLINK format
This function converts PLINK format files into data frames containing genotypes information in proper format
for the model fitting and testing.

Gene‐based association tests to model count data with excessive zeros and rare variants using zero-inflated Poisson/zero-inflated negative Binomial regression framework. This method was originally described by Fan, Sun, and Li in Genetic Epidemiology 46(1):73-86 <doi:10.1002/gepi.22438>.

Xiaomin Liu

ZIM4rv

Gene‐based Association Tests of Zero‐inflated Count Phenotype
for Rare Variants

preprocess_genedata function

<dl><dt>fam_file</dt>
<dd>.fam file in PLINK format</dd>
<dt>dosage_file</dt>
<dd>a dosage file includes dosage information of each variant for all individuals</dd>
<dt>region_file</dt>
<dd>a file listing genetic regions where each row contains chromosome, basepairs and the name of genetic region respectively</dd>
<dt>gene_name</dt>
<dd>a character string of the name of a gene, e.g."CEPT". The name is case-sensitive.</dd></dl>

Arguments

preprocess_genedata — preprocess_genedata

<dl>

<dt>fam_file</dt>
<dd>.fam file in PLINK format</dd>


<dt>dosage_file</dt>
<dd>a dosage file includes dosage information of each variant for all individuals</dd>


<dt>region_file</dt>
<dd>a file listing genetic regions where each row contains chromosome, basepairs and the name of genetic region respectively</dd>


<dt>gene_name</dt>
<dd>a character string of the name of a gene, e.g."CEPT". The name is case-sensitive.</dd>

</dl>

preprocess_genedata: preprocess_genedata

Description

Usage

Value

Arguments

Examples