Description Usage Arguments Value See Also Examples
maturing A1 is the reference allele and A2 is the alternate allele.
1 2 3 4 5 6 7 8 9 | loadResults(
path,
focus,
...,
extraColumns = c(),
.retainSE = deprecated(),
signAdj = deprecated(),
moderatorLevel = deprecated()
)
|
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 |
a data.table with one row per SNP
Other reporting:
isSuspicious()
,
plot.gwsemResult()
,
signifGxE()
,
signif()
1 2 3 4 5 6 7 | 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")
|
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.
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