PLACO taking long time

[rezanurbt]

Dear PLACO developer,
Thank you for this nice software. Below is my script to run PLACO on HPC. It is running for many hours. Is it normal to take long time or it just stuck somewhere. Could you please advice any idea on running it faster?

Thank you much for your help.
Kind regards
Reza

Script:

run_placo.R

setwd("/mnt/lustre/working/lab_michellel/rezanurR/placo_analysis")
source("PLACO_v0.2.0.R")
library(data.table)

Load harmonized file

load("merged_harmonized.RData")

Filter out extreme Z

merged_harmonized <- merged_harmonized[(Z1^2 <= 80) & (Z2^2 <= 80)]

Z.matrix <- as.matrix(merged_harmonized[, .(Z1, Z2)])
P.matrix <- as.matrix(merged_harmonized[, .(p1, p2)])
colnames(P.matrix) <- c("P1", "P2")
VarZ <- var.placo(Z.matrix, P.matrix, p.threshold = 1e-4)

out <- sapply(1:nrow(Z.matrix), function(i) placo(Z = Z.matrix[i, ], VarZ = VarZ))

merged_harmonized[, :=(
T_placo = as.numeric(out["T.placo", ]),
p_placo = as.numeric(out["p.placo", ])
)]

Save results

save(merged_harmonized, file = "placo_output.RData")