wgs_adno_partitioner: Create Data Partitions for LMER Modeling

In Ehyaei/IRISUtils: This package contains many functions that were used in the Hardy Lab Statistical Genetics projects.

Create Data Partitions for LMER Modeling

Description

This function creates data partitions for 'lmer' modeling. To create data, first we load adnimerge and select specific columns. Then we load the WGS PCA data and select the required columns. In the next step, merge the two datasets into one. Finally, we merge WGS data by 'PTID'. Data is melted and created into a tidy version before being used in data.table format.

Usage

wgs_adno_partitioner(
  partition_number = 300,
  clinical_variables = c("MMSE", "GENDER", "AGE", "MMSE.bl", "PTEDUCAT", "PTID",
    "VISID"),
  pca_components = c("PC1", "PC2", "PC3"),
  wgs_path,
  pca_path,
  adni_path,
  partitions_save_path,
  fill_col = NULL
)

Arguments

partition_number	is an integer number that represents the number of data is divided.
clinical_variables	character vector contains names of variables in ADNI clinical data.
pca_components	character vector contains names of variables in WGS PCA data.
wgs_path	is path of ADNI WGS data.
pca_path	is path of PCA components WGS data.
adni_path	is path of adnimerge.RData. It must contains clinical_variables columns.
partitions_save_path	is the save path of data partitions.
fill_col	Fills missing values in selected columns using previous entry.
snp_names_save_path	is the save path of SNP names.

Ehyaei/IRISUtils documentation built on March 29, 2022, 9:46 a.m.