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| author | Alexander_Kabui | 2024-10-29 15:39:55 +0300 |
|---|---|---|
| committer | Alexander_Kabui | 2024-10-29 15:39:55 +0300 |
| commit | 7194eaf537c889c979b34a1f092ba5f2c0a8e030 (patch) | |
| tree | b31db930ab59009614f9fb7fd3a161e44051a3c0 /scripts | |
| parent | da4ae79ddce7c36b48d4bb4ba314503ef9743cd7 (diff) | |
| download | genenetwork3-7194eaf537c889c979b34a1f092ba5f2c0a8e030.tar.gz | |
Refactor: refactor function to calculate error LOD scores.
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 13 |
1 files changed, 10 insertions, 3 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 5decd85..2c38dd4 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -11,6 +11,8 @@ options(stringsAsFactors = FALSE) args = commandArgs(trailingOnly = TRUE) +NO_OF_CORES = 4 + # get the json file path with pre metadata required to create the cross if (length(args) == 0) { @@ -169,9 +171,14 @@ print(Pr) summary(Pr) -#calculate genotyping error LOD scores -error_lod <- calc_errorlod(dataset, Pr, quiet = FALSE, cores = 4) -print(error_lod) +#Function to Calculate genotyping error LOD scores +cat("Calculate genotype error LOD scores\n") +error_lod <- calc_errorlod(dataset, Pr, quiet = FALSE, cores = NO_OF_CORES) +# combine into one matrix +error_lod <- do.call("cbind", error_lod) +print(error_lod + + # Perform genome scan |