snpR_import_wrappers: snpRdata Import Wrappers
In hemstrow/snpR: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data

snpR_import_wrappers

R Documentation

snpRdata Import Wrappers

Description

These functions wrap import.snpR.data to import data into the snpRdata format from a range of file or object sources.

Usage

read_vcf(file, snp.meta = NULL, sample.meta = NULL)

read_ms(file, sample.meta = NULL, chr.length, fix_overlaps = TRUE)

read_delimited_snps(
  file,
  snp.meta = NULL,
  sample.meta = NULL,
  mDat = "NN",
  header_cols = 0
)

read_genepop(file, snp.meta = NULL, sample.meta = NULL, mDat = "0000")

read_FSTAT(file, snp.meta = NULL, sample.meta = NULL, mDat = "0000")

read_plink(file)

read_structure(
  file,
  snp.meta = NULL,
  sample.meta = NULL,
  rows_per_individual = 2,
  marker_names = FALSE,
  header_cols = 0,
  mDat = -9
)

convert_genlight(genlight, snp.meta = NULL, sample.meta = NULL)

convert_genind(genind, snp.meta = NULL, sample.meta = NULL)

convert_vcfR(vcfR, snp.meta = NULL, sample.meta = NULL)

Arguments

`file`	character, path to a file containing genotype data to import.
`snp.meta`	data.frame or character, default NULL. Metadata for each SNP, must have a number of rows equal to the number of SNPs in the dataset. If NULL, a single "snpID" column will be added. If a character, the path to a file containing SNP metadata, one row per SNP, with named columns.
`sample.meta`	data.frame, default NULL. Metadata for each individual sample, must have a number of rows equal to the number of samples in the data set. If NULL, a single "sampID" column will be added. If a character, the path to a file containing sample metadata, one row per sample, with named columns.
`chr.length`	numeric, Specifies chromosome lengths. Note that a single value assumes that each chromosome is of equal length whereas a vector of values gives the length for each chromosome in order.
`fix_overlaps`	Logical, default TRUE. If TRUE, overlapping positions will be checked and fixed during 'ms' file import.
`mDat`	character, defaults "0000", "NN", or "-9" depending on method. Note, if the default is set but the data has genotypes stored in 6 characters, mDat will be set to "000000".
`header_cols`	numeric, default 0. The number of snp metadata columns prior to snp genotypes when importing delimited snps.
`rows_per_individual`	numeric (1 or 2), default 2. Number of rows used for each individual.
`marker_names`	logical, default FALSE. If TRUE, assumes that a header row of marker is present.
`genlight`	genlight object to convert, see `genlight`.
`genind`	genind object to convert, see `genind`.
`vcfR`	vcfR object to convert, see `vcfR`.

Details

These functions are all wrappers for import.snpR.data, and all are technically cross-compatible save read_ms: each other function can actually be called with any of the supported formats (read_vcf can be handed a genlight object without failure). These are supported as separate functions for code readability and for ease of discovery.

See import.snpR.data for more detail.

Functions

read_vcf(): Import .vcf or .vcf.gz files.
read_ms(): Import .ms files.
read_delimited_snps(): Import tab delimited data where genotypes are stored as: NN, 0000, or snp_tab format.
read_genepop(): Import genepop formatted data.
read_FSTAT(): Import FSTAT formatted data.
read_plink(): Import plink bed, bim, and fam data.
read_structure(): Import STRUCTURE data files.
convert_genlight(): Convert adegenet genlight objects.
convert_genind(): Convert adegenet genind objects
convert_vcfR(): Convert adegenet vcfR objects

File import

Supports automatic import of several types of files. Options:

.vcf or .vcf.gz: Variant Call Format (vcf) files, supported via vcfR. If not otherwise provided, snp metadata is taken from the fixed fields in the VCF and sample metadata from the sample IDs. Note that this only imports SNPs with called genotypes!
.ms: Files in the ms format, as provided by many commonly used simulation tools.
NN: SNP genotypes stored as actual base calls (e.g. "AA", "CT").
0000: SNP genotypes stored as four numeric characters (e.g. "0101", "0204").
snp_tab: SNP genotypes stored with genotypes in each cell, but only a single nucleotide noted if homozygote and two nucleotides separated by a space if heterozygote (e.g. "T", "T G").
sn: SNP genotypes stored with genotypes in each cell as 0 (homozygous allele 1), 1 (heterozygous), or 2 (homozyogus allele 2).
genepop: genepop file format, with genotypes stored as either 4 or 6 numeric characters. Works only with bi-allelic data. Genotypes will be converted (internally) to NN: the first allele (numerically) will be coded as A, the second as C.
FSTAT: FSTAT file format, with genotypes stored as either 4 or 6 numeric characters. Works only with bi-allelic data. Genotypes will be converted (internally) to NN: the first allele (numerically) will be coded as A, the second as C.
plink: plink .bed, .fam, and .bim files, via read_plink. If any of these file types is provided, snpR via read_plink will look for the other file types automatically. Sample metadata should be contained in the .fam file and SNP metadata in the .bim file, so sample or snp meta data can be provided here.
structure: STRUCTURE import file, with individuals in rows and loci in columns. Can be coded either with one row per individual and two columns per loci or two rows per individual and two columns per loci using the rows_per_individual argument. Genotypes can be pretty much anything, although missing genotypes must be coded as -9. Must have a .str extension and be consistantly whitespace delimited.

Sample and snp metadata can also be provided via file path, and will be read in using fread with the default settings using read_delimited_snps. If these settings are not correct, please read in the metadata manually and provide to import.snpR.data.

Conversions from other S4 objects

Supports automatic conversions from some other popular S4 object types. Options:

genind: genind objects from adegenet. Note, no need to import genepop objects, the equivalent statistics are calculated automatically when functions called with facets. Sample and SNP IDs as well as, when possible, pop IDs will be taken from the genind object. This data will be added too but will not replace data provided to the SNP or sample.meta arguments. Note that only SNP data is currently allowed, data with more than two alleles for loci will return an error.
genlight: genlight objects from adegenet. Sample and SNP IDs, SNP positions, SNP chromosomes, and pop IDs will be taken from the genlight object if possible. This data will be added too but will not replace data provided to the SNP or sample.meta arguments.
vcfR: vcfR objects from vcfR. If not provided, snp metadata is taken from the fixed fields in the VCF and sample metadata from the sample IDs. Note that this only imports SNPs with called genotypes!