read.snps.long {snpStats} | R Documentation

## Read SNP data in long format (deprecated)

### Description

Reads SNP data when organized in free format as one call per line. Other than the one call per line requirement, there is considerable flexibility. Multiple input files can be read, the input fields can be in any order on the line, and irrelevant fields can be skipped. The samples and SNPs to be read must be pre-specified, and define rows and columns of an output object of class `"SnpMatrix"`. This function has been replaced in versions 1.3 and later by the more flexible function `read.long`.

### Usage

    read.snps.long(files, sample.id = NULL, snp.id = NULL, diploid = NULL,
                  fields = c(sample = 1, snp = 2, genotype = 3, confidence = 4),
                  codes = c("0", "1", "2"), threshold = 0.9, lower = TRUE,
                  sep = " ", comment = "#", skip = 0, simplify = c(FALSE,FALSE),
                  verbose = FALSE, in.order=TRUE, every = 1000)

### Arguments

`files` | A character vector giving the names of the input files
`sample.id` | A character vector giving the identifiers of the samples to be read
`snp.id` | A character vector giving the names of the SNPs to be read
`diploid` | A logical array of the same length as `sample.id`, required if reading data into an `XSnpMatrix` rather than a `SnpMatrix`. This vector gives the expected ploidy for each row. If the same value suffices for all rows, then a scalar may be supplied
`fields` | A integer vector with named elements specifying the positions of the required fields in the input record. The fields are identified by the names `sample` and `snp` for the sample and SNP identifier fields, `confidence` for a call confidence score (if present) and either `genotype` if genotype calls occur as a single field, or `allele1` and `allele2` if the two alleles are coded in different fields
`codes` | Either the single string `"nucleotide"` denoting that coding in terms of nucleotides (`A`, `C`, `G` or `T`, case insensitive), or a character vector giving genotype or allele codes (see below)
`threshold` | A numerical value for the calling threshold on the confidence score
`lower` | If `TRUE`, then `threshold` represents a lower bound. Otherwise it is an upper bound
`sep` | The delimiting character separating fields in the input record
`comment` | A character denoting that any remaining input on a line is to be ignored
`skip` | An integer value specifying how many lines are to be skipped at the beginning of each data file
`simplify` | If `TRUE`, sample and SNP identifying strings will be shortened by removal of any common leading or trailing sequences when they are used as row and column names of the output `SnpMatrix`
`verbose` | If `TRUE`, a progress report is generated as every `every` lines of data are read
`in.order` | If `TRUE`, input lines are assumed to be in the correct order (see details)
`every` | See `verbose`

### Details

If nucleotide coding is not used, the `codes` argument should be a character array giving the valid codes. For genotype coding of autosomal SNPs, this should be an array of length 3 giving the codes for the three genotypes, in the order homozygous(AA), heterozygous(AB), homozygous(BB). All other codes will be treated as "no call". The default codes are `"0"`, `"1"`, `"2"`. For X SNPs, males are assumed to be coded as homozygous, unless an additional two codes are supplied (representing the AY and BY genotypes). For allele coding, the `codes` array should be of length 2 and should specify the codes for the two alleles. Again, any other code is treated as "missing" and, for X SNPs, males should be coded either as homozygous or by omission of the second allele.

For nucleotide coding, nucleotides are assigned to the nominal alleles in alphabetic order. Thus, for a SNP with either "T" and "A" nucleotides in the variant position, the nominal genotypes AA, AB and BB will refer to A/A, A/T and T/T.

Although the function allows for reading into an object of class `XSnpMatrix` directly, it is usually preferable to read such data as a `"SnpMatrix"` (i.e. as autosomal) and to coerce it to an object of type `"XSnpMatrix"` later using `as(..., "X.SnpMatrix")` or `new("XSnpMatrix", ..., diploid=...)`. If `diploid` is coded `NA` for any subject the latter course must be followed, since `NA`s are not accepted in the `diploid` argument.

If the `in.order` argument is set `TRUE`, then the vectors `sample.id` and `snp.id` must be in the same order as they vary on the input file(s) and this ordering must be consistent. However, there is no requirement that either SNP or sample should vary fastest as this is detected from the input. If `in.order` is `FALSE`, then no assumptions about the ordering of the input file are assumed and SNP and sample identifiers are looked up in hash tables as they are read. This option must be expected, therefore, to be somewhat slower. Each file may represent a separate sample or SNP, in which case the appropriate `.id` argument can be omitted; row or column names are then taken from the file names.

### Value

An object of class `"SnpMatrix"` or `"XSnpMatrix"`.

### Note

The function will read gzipped files.

If `in.order` is `TRUE`, every combination of sample and snp listed in the `sample.id` and `snp.id` arguments must be present in the input file(s). Otherwise the function will search for any missing observation until reaching the end of the data, ignoring everything else on the way.

### Author(s)

David Clayton dc208@cam.ac.uk

### See Also

`read.plink`, `SnpMatrix-class`, `XSnpMatrix-class`

[Package snpStats version 1.44.0 Index]