one error at step 3

[kys21207]

Hi CGWAS,

Please see the error below. I am not sure why I met the error.

"Error in summary.connection(connection) : invalid connection"

cgwas(gwasFilePath, snpFilePath, outputPath,
traitName = traitName, mrafFilePath = mrafFilePath, indSNPN = indSNPN)

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/ / / /| | / // | / /
/ / ______ / / __ | | /| / // /| | _
/ //_____// // / | |/ |/ // ___ | / /
_/ _/ |/|/// ||/___/ version 0.9.3

========== C-GWAS basic parameters ==========

GWAS result file path : /home/cdsw/test_cgwas
SNP information file path : ~/test_cgwas/SnpInfo
GWAS name : D1, D2, D3
Exclude NA : TRUE
MRAF path : ~/test_cgwas/mraf
Output path : /home/cdsw
Keep i-EbICoW output : FALSE
Parallel number : 20

========== C-GWAS advanced parameters ==========

User define 2/13 parameters

Independent SNP number : 1e+05
Min EbICoW power increase ratio : 1.1

Other 11/13 parameters are in default

========== C-GWAS step 1 : Data formating ==========

Read and format 3 GWASs ..

0 SNP with NA found
==================================================
--------------------------------------------------
==================================================

C-GWAS step 1 completed
Step 1 takes 104.9 Secs.

========== C-GWAS step 2 : GetI ==========

Estimating inflation for 3 GWASs ..
Adjusted GWASs test statistics written to Details/i-EbICoW/
Summary of GetI written to Details/SummaryGetI.txt

C-GWAS step 2 completed
Step 2 takes 20.3 Secs.

========== C-GWAS step 3 : GetPsi ==========

Estimating background correlation for 3 GWAS pairs ..
Error in summary.connection(connection) : invalid connection

[kys21207]

Code

outputPath <- getwd() # set the directory of the output files
ExDataDir <- "~/test_cgwas"
gwasFileName <- c("d1.assoc", "d2.assoc", "d3.assoc")
gwasFilePath <- file.path(ExDataDir, gwasFileName)
snpFilePath <- file.path(ExDataDir, 'SnpInfo')
traitName <- c("D1", "D2", "D3")

mrafFilePath <- file.path(ExDataDir, 'mraf')
indSNPN = 1e5

cgwas(gwasFilePath, snpFilePath, outputPath,
traitName = traitName, mrafFilePath = mrafFilePath, indSNPN = indSNPN)

[kys21207]

I found the cause in the code below. It looks like you forgot to add 'registerDoParallel(cl)' in step 3. See the updated code below. Now it works well..

GetPsi

step3 <- function(cgwasenv) {
logOutput("========== C-GWAS step 3 : GetPsi ==========\n\n", cgwasenv = cgwasenv)
logOutput("Estimating background correlation for ",
nrow(pairma <- t(combn(seq_len(cgwasenv$.TRAIT_NUM), 2))),
" GWAS pairs ..\n", cgwasenv = cgwasenv)

minsnpn = 1e5
maSpltRw = ceiling(cgwasenv$.SNP_N / minsnpn)
maSpltN = floor(cgwasenv$.SNP_N / maSpltRw) * maSpltRw
resinfm <- as.matrix(
read.table(file.path(cgwasenv$.CGWAS_DETAIL_PATH, "SummaryGetI.txt"),
header = T)[,-1])

threadNCur <- min(cgwasenv$.PARAL_NUM, nrow(pairma))
cl <- makeCluster(threadNCur)
registerDoParallel(cl)

globalVariables(c('i'))

i <- 1 # assign parallel control variants