seqSAIGE_LoadPval: Load the association results

In SAIGEgds: Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies

Description

Load the association results from an RData, RDS 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.rds", 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)

SAIGEgds documentation built on Nov. 8, 2020, 7:46 p.m.