importFile {GeneGeneInteR} | R Documentation

## Imports SNPs information from pedfile, PLINK, VCF (4.0) file, or genotypes imputed by IMPUTE2.

### Description

`importFile` generates a SnpMatrix object on the basis of diallelic object contained in a file, and creates also a data frame containing information about positions of the SNPs on the genome.

### Usage

    importFile(file, pos, pos.sep = "\t", ...)

### Arguments

`file` | String containing the path of the file to import.
`pos` | (optional) Path of a csv file, character vector or numeric vector containing informations for each SNP about chromosome, gene names, snp names and positions.
`pos.sep` | (optional) String to be passed to `read.csv` function as `sep` argument. Default is tab (\t).
`...` | Additionnal arguments to be passed to the reading file function.

### Details

As input information, `importFile` takes the full paths of the files to be imported. Files are then read with `read.pedfile`, `read.plink`, `vcf2sm`, or `read.impute`, depending on the file extension (pedfile, plink, vcf or impute2). For a pedfile, `importFile` also reads the ".info" file associated (this must be in the same directory as the ".ped". Similarly, for a PLINK, there must be 3 files with extensions ".bed" (passed as argument `file`), ".bim" and ".fam". A VCF file must be with the associated ".tbi" file.

If the file is a vcf file, two additional arguments have to done :

- `gr` instance of `GRanges.`

- `nmetacol` numeric defining the number of columns used in each record as locus-level metadata.

`Pos` argument is optional. If it's not given, the data frame with position information is filled with NAs, except for SNP names which are imported from the column names of the SnpMatrix, and eventually positions and chromosomes if the file imported is a pedfile or a PLINK. Else, the `pos` argument can be either the path to a csv file, a character vector with elements of the form chr:position, or a numeric vector with only the positions. Additionnaly, SNP names can be precised as names of the vector. If you choose the csv file path, be sure that the columns are named as follows : Chromosome, Genenames, SNPnames, Position.

### Value

A list of two objects :

``snpX`` | a SnpMatrix
``genes.info`` | a data frame with 4 columns, and one row per SNP. The columns are Chromosome, Genenames, SNPnames and position.

### Examples

    ## Pedfile from this package.
    ped <- system.file("extdata/example.ped", package="GeneGeneInteR")
    info <- system.file("extdata/example.info", package="GeneGeneInteR")

    ## Information about position of the snps
    posi <- system.file("extdata/example.txt", package="GeneGeneInteR")

    ## Importation
    data.imported <- importFile(file=ped, snps=info, pos=posi, pos.sep="\t")

    #########
    ## VCF file from GGtools package.
    ## Not run:
    vref <- system.file("vcf/CEU.exon.2010_09.genotypes.vcf.gz", package="GGtools")
    irange <- IRanges::IRanges(10e6,20e6)
    gg = GenomicRanges::GRanges(seqnames="1", ranges=irange)
    dta <- importFile(file=vref, gr=gg, nmetacol=9L)

    ## End(Not run)

[Package GeneGeneInteR version 1.10.0 Index]