readStandardGenotypes: Read genotypes from file.

Description

readStandardGenotypes can read genotypes from a number of input formats for standard GWAS (binary plink, snptest, bimbam, gemma) or simulation software (binary plink, hapgen2, genome). Alternatively, simple text files (with specified delimiter) can be read. For more information on the different file formats see External genotype software and formats.

Usage

readStandardGenotypes(
  N,
  filename,
  format = NULL,
  verbose = TRUE,
  sampleID = "ID_",
  snpID = "SNP_",
  delimiter = ","
)

Arguments

Number [integer] of samples to simulate.

filename

path/to/genotypefile [string] in plink, oxgen (impute2/snptest/hapgen2), genome, bimbam or [delimiter]-delimited format ( for format information see External genotype software and formats).

format

Name [string] of genotype file format. Options are: "plink", "oxgen", "genome", "bimbam" or "delim".

verbose

[boolean] If TRUE, progress info is printed to standard out.

sampleID

Prefix [string] for naming samples (will be followed by sample number from 1 to N when constructing id_samples).

snpID

Prefix [string] for naming SNPs (will be followed by SNP number from 1 to NrSNP when constructing id_snps).

delimiter

Field separator [string] of genotype file when format == "delim".

Value

Named list of [NrSamples X NrSNPs] genotypes (genotypes), their [NrSNPs] SNP IDs (id_snps), their [NrSamples] sample IDs (id_samples) and format-specific additional files (such as format-specific genotypes encoding or sample information; might be used for output writing).

External genotype software and formats

Formats:

PLINK: consists of three files: .bed, .bim and .fam. When specifying the filepath, only the core of the name without the ending should be specified (i.e. for geno.bed, geno.bim and geno.fam, geno should be specified). When reading data from plink files, the absolute path to the plink-format file has to be provided, tilde expansion not provided. From https://www.cog-genomics.org/plink/1.9/formats: The .bed files contain the primary representation of genotype calls at biallelic variants in a binary format. The .bim is a text file with no header line, and one line per variant with the following six fields: i) Chromosome code (either an integer, or 'X'/'Y'/'XY'/'MT'; '0' indicates unknown) or name, ii) Variant identifier, iii) Position in morgans or centimorgans (safe to use dummy value of '0'), iv) Base-pair coordinate (normally 1-based, but 0 ok; limited to 231-2), v) Allele 1 (corresponding to clear bits in .bed; usually minor), vi) Allele 2 (corresponding to set bits in .bed; usually major). The .fam file is a text file with no header line, and one line per sample with the following six fields: i) Family ID ('FID'), ii), Within- family ID ('IID'; cannot be '0'), iii) Within-family ID of father ('0' if father isn't in dataset, iv) within-family ID of mother ('0' if mother isn't in dataset), v) sex code ('1' = male, '2' = female, '0' = unknown), vi) Phenotype value ('1' = control, '2' = case, '-9'/'0'/non-numeric = missing data if case/control)
oxgen: consists of two files: the space-separated genotype file ending in .gen and the space-separated sample file ending in .sample. When specifying the filepath, only the core of the name without the ending should be specified (i.e. for geno.gen and geno.sample, geno should be specified). From https://www.well.ox.ac.uk/~gav/snptest/#input_file_formats: The genotype file stores data on a one-line-per-SNP format. The first five entries of each line should be the SNP ID, RS ID of the SNP, base-pair position of the SNP, the allele coded A and the allele coded B. The SNP ID can be used to denote the chromosome number of each SNP. The next three numbers on the line should be the probabilities of the three genotypes AA, AB and BB at the SNP for the first individual in the cohort. The next three numbers should be the genotype probabilities for the second individual in the cohort. The next three numbers are for the third individual and so on. The order of individuals in the genotype file should match the order of the individuals in the sample file. The sample file has three parts (a) a header line detailing the names of the columns in the file, (b) a line detailing the types of variables stored in each column, and (c) a line for each individual detailing the information for that individual. For more information on the sample file visit the above url or see writeStandardOutput.
genome: The entire output of genome can be saved via `genome -options > outputfile`. The /path/to/outputfile should be provided and this function extracts the relevant genotype information from this output file. http://csg.sph.umich.edu/liang/genome/
bimbam: Mean genotype file format of bimbam which is a single, comma- separated file, without information on individuals. From the documentation for bimbam at http://www.haplotype.org/software.html: the first column of the mean genotype files is the SNP ID, the second and third columns are allele types with minor allele first. The remaining columns are the mean genotypes of different individuals <U+2013> numbers between 0 and 2 that represents the (posterior) mean genotype, or dosage of the minor allele.
delim: a [delimter]-delimited file of [(NrSNPs+1) x (NrSamples+1)] genotypes with the snpIDs in the first column and the sampleIDs in the first row and genotypes encoded as numbers between 0 and 2 representing the (posterior) mean genotype, or dosage of the minor allele. Can be user-genotypes or genotypes simulated with foward-time algorithms such as simupop (http://simupop.sourceforge.net/Main/HomePage) that allow for user-specified output formats.

Genotype simulation characteristics:

PLINK: simple, bi-allelelic genotypes without LD structure, details can be found at https://www.cog-genomics.org/plink/1.9/input#simulate.
Hapgen2: resampling-based genotype simulation, details can be found at http://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html.
Genome: coalescent-based genotype simulation, details can be found at http://csg.sph.umich.edu/liang/genome/GENOME-manual.pdf.

Examples on how to call these genotype simulation tools can be found in the vignette sample-scripts-external-genotype-simulation.

Details

The file formats and software formates supported are described below. For large external genotypes, consider the option to only read randomly selected, causal SNPs into memory via getCausalSNPs.

Examples

Run this code

# NOT RUN {
# Genome format
filename_genome  <- system.file("extdata/genotypes/genome/",
"genotypes_genome.txt",
package = "PhenotypeSimulator")
data_genome <- readStandardGenotypes(N=100, filename_genome, format ="genome")

filename_hapgen  <- system.file("extdata/genotypes/hapgen/",
"genotypes_hapgen.controls.gen",
package = "PhenotypeSimulator")
filename_hapgen <- gsub("\\.gen", "", filename_hapgen)
data_hapgen <- readStandardGenotypes(N=100, filename_hapgen, format='oxgen')

filename_plink  <- system.file("extdata/genotypes/plink/",
"genotypes_plink.bed",
package = "PhenotypeSimulator")
filename_plink <- gsub("\\.bed", "", filename_plink)
data_plink <- readStandardGenotypes(N=100, filename=filename_plink,
format="plink")

filename_delim  <- system.file("extdata/genotypes/",
"genotypes_chr22.csv",
package = "PhenotypeSimulator")
data_delim <- readStandardGenotypes(N=50, filename=filename_delim,
format="delim")
# }

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