loadResults: Load GWAS results into a single data.frame

In gwsem: Genome-Wide Structural Equation Modeling

Description

\lifecycle

maturing A1 is the reference allele and A2 is the alternate allele.

Usage

loadResults(
  path,
  focus,
  ...,
  extraColumns = c(),
  .retainSE = deprecated(),
  signAdj = deprecated(),
  moderatorLevel = deprecated()
)

Arguments

path	vector of paths to result files created by GWAS
focus	parameter name on which to calculate a Z score and p-value
...	Not used. Forces remaining arguments to be specified by name.
extraColumns	character vector of additional columns to load
.retainSE	logical. Keep a column for the SE of the focus parameter
signAdj	name of column. Value of focus parameter is multiplied by the sign of the named column
moderatorLevel	\lifecycle deprecated

Value

a data.table with one row per SNP

See Also

Other reporting: isSuspicious(), plot.gwsemResult(), signifGxE(), signif()

Examples

tdir <- tempdir()
dir <- system.file("extdata", package = "gwsem")
pheno <- data.frame(anxiety=rnorm(500))
m1 <- buildItem(pheno, 'anxiety')
GWAS(m1, file.path(dir,"example.bgen"),
    file.path(tdir,"out.log"))
loadResults(file.path(tdir,"out.log"), "snp2anxiety")

Example output

Loading required package: OpenMx
sh: 1: wc: Permission denied
To take full advantage of multiple cores, use:
  mxOption(key='Number of Threads', value=parallel::detectCores()) #now
  Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)

Attaching package: ‘gwsem’

The following object is masked from ‘package:base’:

    signif

Running OneItem with 3 parameters
Done. See '/work/tmp/tmp/Rtmp9FxOal/out.log' for results
     MxComputeLoop1 CHR     BP       SNP A1 A2 statusCode catch1
  1:              1   1   1001 SNPID_101  G  A         OK       
  2:              2   1   2000   SNPID_2  G  A         OK       
  3:              3   1   2001 SNPID_102  G  A         OK       
  4:              4   1   3000   SNPID_3  G  A         OK       
  5:              5   1   3001 SNPID_103  G  A         OK       
 ---                                                            
195:            195   1  98000  SNPID_98  G  A         OK       
196:            196   1  98001 SNPID_198  G  A         OK       
197:            197   1  99000  SNPID_99  G  A         OK       
198:            198   1  99001 SNPID_199  G  A         OK       
199:            199   1 100001 SNPID_200  G  A         OK       
Warning messages:
1: In fread(p1, header = TRUE, sep = "\t", check.names = FALSE, quote = "",  :
  Column name 'snp2anxiety' not found in column name header (case sensitive), skipping.
2: In fread(p1, header = TRUE, sep = "\t", check.names = FALSE, quote = "",  :
  Column name 'Vsnp2anxiety:snp2anxiety' not found in column name header (case sensitive), skipping.

gwsem documentation built on Jan. 18, 2022, 1:09 a.m.