filter_subset: Subset Dataset Based on Filter Results
In jillbo1000/gwas3: Three Phase Filtering for GWAS

filter_subset uses the original genotypes and the vector returned by snp_filter to create a new dataset that contains only the variables that pass through the user-specified threshold for p-values or distance correlations. If a window is used, the returned dataset will include all of the SNPs in a window for a SNP that meets the threshold.

1	filter_subset(x, results, type = "dc", threshold, window = 1)

`x`	A matrix or dataset containing the genotypes for each observation. The number of variables must match the number of elements in the `results` vector.
`results`	A vector of p-values or distance correlations, preferably the output vector from the `snp_filter` function. The length of `results` must be equal to the number of variables in `x`.
`type`	The type of measure in the results vector. The default is "dc" for distance correlations. If a different string is used it is assumed that the vector contains p-values.#'
`threshold`	This value can either be decimal less than 1 or a positive integer. If a number less than 1 and if the results are p-values, all SNPs with a p-value less than the threshold will be retained. If the results are distance correlations, all SNPs with a value greater than the threshold will be retained. A positive integer indicates how many SNP should pass through the filter.
`window`	This is the size of the window used in the initial filter. If a window was used in the `snp_filter` function. The dataset that is returned will contain the selected SNP and the SNPs in the window around the SNP.

Returns a dataset that contains the SNPs that pass through the user specified threshold. The output can be used directly as an input into the elasticnet function in this package.

jillbo1000/gwas3 documentation built on June 14, 2019, 3:08 a.m.