snpMatrixScour {GeneGeneInteR} | R Documentation

## SNP filtering based on Minor Allele Frequency, Hardy-Weinberg Equilibrium and call rate

### Description

`snpMatrixScour` aims at filtering out SNPs of a snpMatrix object based on Minor Allele Frequency criterion, deviation to Hardy-Weinberg Equilibrium and SNPs call rate.

### Usage

    snpMatrixScour(snpX, genes.length = NULL, genes.info = NULL,
      min.maf = 0.01, min.eq = 0.01, call.rate = 0.9)

### Arguments

`snpX` | SnpMatrix object from which SNPs are to be removed
`genes.length` | (optional) numeric vector. It is the length (in columns/SNPs) of each gene. Each gene declared is considered contiguous with the one before and after it. `genes.lengths` can be named (names will be kept).
`genes.info` | (optional) a `data.frame` with four columns named `Genenames`, `SNPnames`, `Position` and `Chromosome`. Each row describes a SNP and missing values are not allowed.
`min.maf` | a single value between 0 and 0.5 that gives the threshold for the MAF (Minor Allele Frequency) of a SNP. SNP with MAF < `min.maf` are removed. Default is 0.01.
`min.eq` | a single value between 0 and 1 that gives the maximum acceptable p-value for the χ ^2 verifying HWE deviation. SNP that does not meet that criterion are removed. Default is 0.01.
`call.rate` | a single value between 0 and 1 that gives the minimum acceptable call rate for a SNP. Default is 0.9. Low values for SNPs call rate can make imputation harder (residual missing values).

### Details

This function removes SNPs that does not meet all following criteria:

- MAF < `min.maf`,

- HWE < `min.eq`, where HWE is the p-value of the χ ^2 test of deviation to Hardy-Weinberg Equilibrium,

- Call rate > `call.rate`.

If `genes.length` and `genes.info` are provided by the user, an updated version is returned by `snpMatrixScour`. The returned object can be directly used as inputs of the `GGI` function.

### Value

A list with two objects:

`snpX`

  the SnpMatrix object where non-conform SNPs are removed.

`genes.info`

  the object that contains the updated gene lengths information. Can be a numeric vector (possibly named) or a data frame. If `genes.length` and `genes.info` are not provided by the user as input of the `snpMatrixScour` function, the `genes.info` object is `NULL`.

### See Also

`GGI`

### Examples

    ## Not run:
    ped <- system.file("extdata/example.ped", package="GeneGeneInteR")
    info <- system.file("extdata/example.info", package="GeneGeneInteR")
    posi <- system.file("extdata/example.txt", package="GeneGeneInteR")
    data.imported <- importFile(file=ped, snps=info, pos=posi, pos.sep="\t")

    ## End(Not run)
    ### Equivalent loading of the imported data
    load(system.file("extdata/dataImported.Rdata", package="GeneGeneInteR"))

    ## In this example, SNPs are with MAF lower than 0.2 or p-value for HWE testing lower than 0.05 or
    # a proportion of missing value higher than 0.2 are removed
    data.scour1 <- snpMatrixScour(data.imported$snpX, genes.info = data.imported$genes.info,
                                   min.maf = 0.2, min.eq=0.05, call.rate = 0.8)
    ## Two genes have been completely removed from the resulting dataset.

[Package GeneGeneInteR version 1.16.0 Index]