louise
commented
9 months ago Hi, I'm not sure what the issue is, but I can take a look if you send across the results files. Feel free to send them via email – louise.millard@bristol.ac.uk.
Best wishes, Louise
Hello， I am currently using the phenomeScan.r script from the PHESANT package and have encountered an issue when running mainCombineResults.r. I have successfully run it and got the QQ plot, but the forest plot I got is blank. Do you have any suggestions on how to solve this problem? Thank you for your assistance.
Rscript /PHESANT-master/resultsProcessing/mainCombineResults.r \ --resDir="/test/result/1/" \ --variablelistfile="/PHESANT-master/variable-info/outcome-info.tsv" \ --numParts=5 WARNING: ignoring environment value of R_HOME [1] "Finished flow counts" [1] "Finished combining results" Warning message: In read.table(dcfile, header = 1, sep = "\t", comment.char = "", : incomplete final line found by readTableHeader on '../ukb_data_codes/data_codes/datacode-227.tsv' [1] "Finished adding variable descriptions to results listing" [1] "Number not exposure variable: 5471" [1] "Bonferroni threshold: 9.13909705721075e-06" [1] "Number below Bonferroni threshold: 28" [1] "Finished QQ plot" Loading required package: grid Loading required package: checkmate Loading required package: abind [1] "Number below Bonferroni threshold: 28" [1] "Making forest plot for: binary" [1] "Number below Bonferroni threshold: 26" [1] "Finished forest plot" [1] "Making forest plot for: continuous" [1] "Number below Bonferroni threshold: 2" [1] "Finished forest plot" [1] "Making forest plot for: ordered-logistic" [1] "Number below Bonferroni threshold: 0" [1] "Forest plot not made." [1] "Number of MULTINOMIAL-LOGISTIC results (that we do not make a forest plot for): 0"