snp.list {CGEN} | R Documentation

## List to describe the genotype data

### Description

The list to describe the genotype data for `GxE.scan`.

### Format

The format is: List of 14

file

  File to use. No default.

format

  Genotype format (see details). Typical values are "bed", "tped", "impute", "ldat", "lbat", etc. The default is determined from the `file` extension.

subject.list

  List to describe the subject ids stored in a file. This list is only needed when the genotype file does not contain the subject ids (for example with PLINK files). The order of the subject ids is `subject.list$file` must match the order in the genotype data. See `subject.list`. The default is NULL.

start.vec

  Starting row of `file` to begin processing SNPs. The default is 1.

stop.vec

  Last row of `file` to finish processing SNPs. Use any value < 1 so that all SNPs from rows `start.vec` to the end of the file will be analyzed. The default is -1.

delimiter

  The delimiter used in `file`. The default is determined from the `file` format.

in.miss

  Vector of values to denote the missing values in `file`. The default is determined from the `file` format.

heter.codes

  Vector of codes used for the heterozygous genotype. If NULL, then it is assumed that the heterozygous genotype is of the form "AB", "Aa", "CT", ... etc, ie a 2-character string with different characters (case sensitive). The default is NULL.

Options only used with `GxE.scan`:

include.snps

  File, list or character vector to define which SNPs should be included in the analysis. If a file, then the file should contain a single column of SNP ids to include. More generally, if the SNPs to be included are in a file with multiple columns, then `include.snps` can be a list of type `subject.list`. If it is a character vector, then it should be a vector of SNP ids. This option can also be used with the options `start.vec` and `stop.vec` (see details). The default is NULL.

PLINK

  Command for running the PLINK software to transform certain `file` formats (see details). Set PLINK to "" if PLINK is not available or if you do not want PLINK to be used.
  The PLINK software can be found at http://pngu.mgh.harvard.edu/~purcell/plink/. The default is "plink".

GLU

  Command for running the GLU software to transform certain `file` formats (see details). Set GLU to "" if GLU is not available or if you do not want GLU to be used.
  The GLU software can be found at http://code.google.com/p/glu-genetics/. The default is "glu".

### Details

In this list, `file` must be specified, and `format` should be specified. If not, then the program will attempt to guess the correct `format` of the genotype data from the file extension of `file`. If `format` is a format that `GxE.scan` is not set up to read directly (such as "bed", "lbat", "ped"), then either PLINK or GLU will be called to transform the data into either a "tped" or "ldat" format. When the option `include.snps` is specified as a file, then the options `start.vec` and `stop.vec` will be applied to the SNPs in this file. For example, suppose we have the genotype file snps.bed which is the PLINK "bed" format. We can set `include.snps` to the corresponding ".bim" file:
include.snps <- list(file="snps.bim", id.var=2, header=0, delimiter="\t"). Then the included SNPs in the analysis will be the SNPs in rows `start.vec` to `stop.vec` of file "snps.bim".

Other options such as `delimiter` and `in.miss` do not need to be specified, because they can be determined from the genotype data format. If the SNPs are coded in the standard (0,1,2) coding, then set `heter.codes` to 1 (the heterozygous genotype).

### Examples

    # Example snp.list for a PLINK binary pedigree file when using GxE.scan
    ## Not run:
    pathToPLINK  <- "c:/PLINK/plink-1.07-dos/plink.exe"
    snp.file     <- "c:/data/project1/lungCancer.bed"
    subject.list <- "c:/data/project1/lungCancer.fam"
    snp.list <- list(file=snp.file, format="bed", PLINK=pathToPLINK,
                     subject.list=subject.list)

    ## End(Not run)

    # Suppose the genotype data is an output genotype file from th IMPUTE2 software
    # The below list is for processing the file.
    ## Not run:
    snp.list <- list(file="C:/temp/data/chr11_1.imputed.txt.gz", delimiter=" ", format="impute")

    ## End(Not run)

[Package CGEN version 3.20.0 Index]