toArray: Turn Illumina's Genome Studio ‘Final Report’ file into an array

Description

toArray is a function to turn genotyping data into an array. This function does not read stored data in the ‘Final Report’ file, however, it converts a data fram with the same structure as ‘Final Report’ into an object of class matrix. The specifications of the genotyping data frame are given under ‘Details’.

Usage

toArray(finalRep)

Arguments

finalRep

A data frame with the same structure as ‘Final Report’, containing genotyping data. Specifications are given under ‘Details’.

Value

An object of class matrix with ‘number of rows = number of individuals’ and ‘number of columns = number of SNPs’. Each element of the matrix consists of a two-character string for the two DNA bases of a single SNP locus.

Details

Used to turn Illumina's Genome Studio ‘Final Report’ file into an array. Specifications of the input data fram, ‘finalRep’, are:

Input is a data frame with its first 4 columns listed in the following order:
1. SNP names, as factor, with equal number of SNPs per individual.
2. Identification codes, as factor, for genotyped individuals.
3. Allele 1 (one character: A, C, G, T, or -).
4. Allele 2 (one character: A, C, G, T, or -).
All SNPs of individual 1 are listed first followed by SNPs of individual 2, and so on.
SNPs are listed for each individual in the same order.

Note that it is easy to read the ‘Final Report’ file into a data frame which is then used as an input to toArray. See ‘Examples’.

Examples

Run this code

# NOT RUN {
## Read file './Final.Report', located in the current working directory,
## and place the first 4 columns in a data frame.

#d <- read.table("./Final.Report", skip=10)[,1:4]

## Use toArray to turn data read into a matrix

#ga <- toArray(finalRep = d)
#ga[1:6, 4000:4002]

#
#               SNP.4000           SNP.4001           SNP.4002
#Individual.1       "GG"               "CC"               "CC"
#Individual.2       "TG"               "AC"               "CC"
#Individual.3       "TG"               "AA"               "CC"
#Individual.4       "GG"               "AC"               "TC"
#Individual.5       "GG"               "AC"               "CC"
#Individual.6       "GG"               "AA"               "CC"
#
# }