Generate_SSD_SetID_wEC: Generate SNP set data file (SSD) with using external control...

Description Usage Arguments Details Author(s)

View source: R/iECAT_SSD.R

Description

Generate SNP set data (SSD) and external control information files

Usage

1
2
3
4
5
 
 	Generate_SSD_SetID_wEC(File.Bed, File.Bim, File.Fam, File.SetID
 	, File.EC, File.SSD, File.Info, File.EC.Info)

 

Arguments

File.Bed

name of the binary ped file (BED).

File.Bim

name of the binary map file (BIM).

File.Fam

name of the FAM file (FAM).

File.SetID

name of the SNP set ID file that defines SNP sets. The first column must be Set ID, and the second column must be SNP ID. There should be no header!!

File.EC

name of the file that has allele count information of the external controls.

File.SSD

name of the SSD file generated.

File.Info

name of the SSD info file generated.

File.EC.Info

name of the external control info file generated.

Details

The SetID file is a white-space (space or tab) delimitered file with 2 columns: SetID and SNP_ID.

Please keep in mind that there should be no header! The SNP_IDs and SetIDs should be less than 50 characters, otherwise, it will return an error message.

File.EC should be a text formated file

The SSD file is a binary formated file with genotypes. The SSD info file is a text file with general information on data and SNP sets (first 6 rows), and information on each set (after 8th row).

Author(s)

Seunggeun Lee, Larisa Miropolsky


leeshawn/iECAT documentation built on Oct. 10, 2020, 3:29 p.m.