setUpGenoDatFile: Loads genotype data onto R

In inveRsion: Inversions in genotype data

Description

Loads onto an R session genotype data from text files or PLINK files.

Usage

setUpGenoDatFile(file = "GenoDat.txt", saveRes = FALSE, sortMinor = TRUE)
setUpGenoDatSNPmat(Chr, Geno, Annot, saveRes = FALSE, saveGeno = FALSE)

Arguments

file	character. File path with genotype information
saveRes	logical. Wether results should be saved into file gDat.RData
sortMinor	logical. Whether genotypes should be sorted by minor allele frequency.
Chr	numeric. Chromosome number
Geno	snpMatrix. Matrix of raw with genotype data
Annot	numeric. Annotation information read from an .bim file
saveGeno	logical. Wether .txt file should be saved with genotype information

Value

GenoDat object

Author(s)

Alejandro Caceres [e-mail]

See Also

GenoDat

Examples

gen <- system.file("extdata", "genotypes.txt", package = "inveRsion")
gDat <-setUpGenoDatFile(file=gen,sortMinor=TRUE,saveRes=FALSE)
gDat

Example output

Loading required package: haplo.stats


Hola!

welcome to inevRsion package. 
 
 

type: manual() for full manual 
      vignette("inveRsion") for a quick start 

-processing data from file:/usr/local/lib/R/site-library/inveRsion/extdata/genotypes.txt-
  reading file ...
  setting: common allele=0, variant allele=1
  setting up GenoDat
-Set up object of class: GenoDat- 
-Showing object of class: GenoDat- 

@genoDat: Genotype Data
   * integer matrix ~ 9 subjects by  10 probes
   * first elements = 
   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
V1 0    1    1    0    1    0    1    1    0    0    
V2 1    0    1    1    1    0    0    1    0    0    
V3 0    0    2    0    2    0    0    2    0    0    
V4 1    0    1    1    1    0    0    1    0    0    
V5 0    0    1    1    1    0    0    1    0    0    
V6 0    0    0    0    0    0    0    0    0    0    
V7 1    0    0    0    0    1    0    0    1    1    
V8 0    0    2    0    2    0    0    2    0    0    
V9 0    0    0    0    1    0    0    1    0    0    

@lociPos: Probe Corrdinates
   * integer ~ 10 probes 
   * first 10 elements = 
  V1   V2   V3   V4   V5   V6   V7   V8   V9  V10 
 959 1268 1393 1467 1531 1761 1847 1987 2006 2030 

Other slots... 

@allaleSum: allele sum at each probe 
@noMissCount: number of no missings values 

-end showing GenoDat- 

inveRsion documentation built on Nov. 8, 2020, 5:08 p.m.