seqSAIGE_LoadPval {SAIGEgds} | R Documentation

## Load the association results

### Description

Load the association results from an RData or GDS file.

### Usage

    seqSAIGE_LoadPval(fn, varnm=NULL, index=NULL, verbose=TRUE)

### Arguments

`fn` | RData, RDS or GDS file names, merging datasets if multiple files
`varnm` | NULL, or a character vector to include the column names; e.g., `c("chr", "position", "rs.id", "ref", "alt", "pval")`
`index` | NULL, or a logical/numeric vector for a set of rows
`verbose` | if `TRUE`, show information

### Value

Return a `data.frame` including p-values.

### Author(s)

Xiuwen Zheng

### See Also

`seqFitNullGLMM_SPA`, `seqAssocGLMM_SPA`

### Examples

    (fn <- system.file("unitTests", "saige_pval.rda", package="SAIGEgds"))
    pval <- seqSAIGE_LoadPval(fn)

    names(pval)
    #  [1] "id"         "chr"        "pos"        "rs.id"      "ref"
    #  [6] "alt"        "AF.alt"     "AC.alt"     "num"        "beta"
    # [11] "SE"         "pval"       "pval.noadj" "converged"

    head(pval)

[Package SAIGEgds version 1.2.3 Index]