snpdata_mgmt: SNP Data Management
In cmcouto-silva/gt: Facilities for essential tasks in R

Description Usage Arguments Value Author(s) Examples

Remove SNPs with duplicated positions, as well as no congruent match to reference table. It provides the possibility of updating missing alleles (0 to the correspondent allele) and SNP IDs ( RefSNP (rs), and Affymetrix ID (Affy), if there is no information for RefSNP).

snpdata_mgmt(
  bim_file,
 
    Affx_HuOrigin = "~/cmcouto.silva@usp.br/lab_files/datasets/Reference_annotation/Affymetrix/Axiom_GW_HuOrigin.na35.annot.csv",
  update_snpID = T,
  update_alleles = T,
  remove_dup_pos = F
)

`bim_file`	Character. Name of bim file.
`Affx_HuOrigin`	Character. <path_to> Axiom_GW_HuOrigin table, available for download at: https://www.thermofisher.com/br/en/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-annotation-files.html
`update_snpID`	Logical. Informs if SNPs will be named according to the reference information (default = TRUE).
`update_alleles`	Logical. Informs if SNPs with zeros will be updated to its basis (default = TRUE).
`remove_dup_pos`	Logical. Informs if duplicated SNPs in dataset would be removed (via Plink Software); otherwise, if any duplicated positions is present on dataset, this function will not progress. Default set to FALSE.

.bim file with updated SNP IDs

Cainã Max Couto-Silva

## Not run: 

bim_file <- "myfile.bim"
Affx_HuOrigin <- "Axiom_GW_HuOrigin.na35.annot.csv"

# Running function
snpdata_mgmt(bim_file, Affx_HuOrigin)

## End(Not run)