Commit 0b9fd5a0 authored by Gael  MILLOT's avatar Gael MILLOT
Browse files

v4.0.0 release

parent a9029f3f
......@@ -25,7 +25,7 @@ Download the desired Tagged version, never the current master.
Open rogge_12231.conf
Set the parameters
Start the job using a command like:
STARTTIME_SH=$(date) ; JOB_ID_SH=$(date -d "$STARTTIME_SH" +%s) ; sh /pasteur/homes/gmillot/Git_versions_to_use/rogge_12231-v1.0.0/rogge_12231_workflow.sh -c /pasteur/homes/gmillot/Git_versions_to_use/rogge_12231-v1.0.0/rogge_12231.conf | tee /pasteur/homes/gmillot/rogge12231/${JOB_ID_SH}_workflow_log
STARTTIME_SH=$(date) ; JOB_ID_SH=$(date -d "$STARTTIME_SH" +%s) ; sh /pasteur/homes/gmillot/Git_versions_to_use/rogge_12231-v4.0.0/rogge_12231_workflow.sh -c /pasteur/homes/gmillot/Git_versions_to_use/rogge_12231-v4.0.0/rogge_12231.conf | tee /pasteur/homes/gmillot/rogge12231/${JOB_ID_SH}_workflow_log &
#### FILE DESCRIPTION
......@@ -60,6 +60,11 @@ Check for updated versions (most recent tags) at https://gitlab.pasteur.fr/gmill
#### WHAT'S NEW IN
## v4.0.0
bug fixed for the Limma analysis and for the valid_boot kind of analysis
## v3.0.0
rogge_12231_main_analysis.R file modified to fit with the new 194samples_67training_13replication_normalized_LR20022019.txt data file
......
......@@ -41,9 +41,9 @@ if(any(duplicated(param.list))){
}
char.length <- nchar(param.list)
space.add <- max(char.length) - char.length + 5
param.ini.settings <- NULL
param.ini.settings <- character(length = length(param.list))
for(i in 1:length(param.list)){
param.ini.settings <- c(param.ini.settings, paste0("\n", param.list[i], paste0(rep(" ", space.add[i]), collapse = ""), paste0(get(param.list[i]), collapse = ",")))
param.ini.settings[i] <- paste0("\n", param.list[i], paste0(rep(" ", space.add[i]), collapse = ""), paste0(get(param.list[i]), collapse = ","))
}
################################ End Recording of the initial parameters
......@@ -68,7 +68,7 @@ analysis.kind <- "full_cross_validation"
activate.pdf <- FALSE # graph file parameter
cut.off.freq.for.selected.genes <- 0.01 # graph file parameter
'
eval(parse(text = debug2)) ; cat(paste0("\n\n================\n\nERROR: ACTIVE DEBUG VALUES\n\n================\n\n")) ; stop()
# eval(parse(text = debug2)) ; cat(paste0("\n\n================\n\nERROR: ACTIVE DEBUG VALUES\n\n================\n\n")) ; stop()
# data.frame(PARAM = tempo.arg.names, ARG = args) # for debug mode
......
......@@ -42,9 +42,9 @@ if(any(duplicated(param.list))){
}
char.length <- nchar(param.list)
space.add <- max(char.length) - char.length + 5
param.ini.settings <- NULL
param.ini.settings <- character(length = length(param.list))
for(i in 1:length(param.list)){
param.ini.settings <- c(param.ini.settings, paste0("\n", param.list[i], paste0(rep(" ", space.add[i]), collapse = ""), paste0(get(param.list[i]), collapse = ",")))
param.ini.settings[i] <- paste0("\n", param.list[i], paste0(rep(" ", space.add[i]), collapse = ""), paste0(get(param.list[i]), collapse = ","))
}
################################ End Recording of the initial parameters
......@@ -94,7 +94,7 @@ analysis.kind <- "valid_boot"
cross.valid.ratio <- 0.8
random.seed <- TRUE
'
eval(parse(text = debug2)) ; cat(paste0("\n\n================\n\nERROR: ACTIVE DEBUG VALUES\n\n================\n\n")) ; stop()
# eval(parse(text = debug2)) ; cat(paste0("\n\n================\n\nERROR: ACTIVE DEBUG VALUES\n\n================\n\n")) ; stop()
# data.frame(PARAM = tempo.arg.names, ARG = args) # for debug mode
......@@ -250,7 +250,9 @@ if(random.seed == TRUE){
used.set.seed <- sample(x = 0:(2^31-1), size = 1)
}else{
used.set.seed <- 1
cat(paste0("\n\n================\n\nBEWARE: NON RANDOM set.seed(1) FUNCTION ACTIVATED \n\n================\n\n"))
tempo.cat <- paste0("\n\n================\n\nBEWARE: NON RANDOM set.seed(1) FUNCTION ACTIVATED \n\n================\n\n")
cat(tempo.cat)
fun_export_data(path = path.out, data = tempo.cat, output = log.file)
}
set.seed(used.set.seed)
backup.name <- c(backup.name, "used.set.seed")
......@@ -338,7 +340,7 @@ if(analysis.kind == "longit"){
if(slurm.loop.nb > 1){
path.loop1 <- gsub(x = path.out, pattern = "loop[1234567890]+", replacement = "loop1") # required for analysis.kind == "valid_boot" training set recovery
}
backup.name <- c(backup.name, "train", "valid")
################ 3 Differential analysis with limma
......@@ -410,6 +412,7 @@ fun_export_data(path = path.out, data = "################################ RANDOM
dat.train <- dat[train, ] # Y and nanostring genes columns of LPS and SEB for the training lines (67 indiv)
dat.valid <- dat[valid, ] # Y and nanostring genes columns of LPS and SEB for the validation lines (9 indiv)
backup.name <- c(backup.name, "dat.train", "dat.valid")
if(any((analysis.kind == "longit" & slurm.loop.nb == 1) | (analysis.kind == "valid_boot" & slurm.loop.nb == 1) | (analysis.kind == "full_cross_validation"))){
# dat.train <- dat[train, ] # Y and nanostring genes columns of LPS and SEB for the training lines (67 indiv)
......@@ -589,7 +592,9 @@ if(random.seed == TRUE){
used.set.seed2 <- sample(x = 0:(2^31-1), size = 1)
}else{
used.set.seed2 <- 1
cat(paste0("\n\n================\n\nBEWARE: NON RANDOM set.seed(1) FUNCTION ACTIVATED \n\n================\n\n"))
tempo.cat <- paste0("\n\n================\n\nBEWARE: NON RANDOM set.seed(1) FUNCTION ACTIVATED \n\n================\n\n")
cat(tempo.cat)
fun_export_data(path = path.out, data = tempo.cat, output = log.file)
}
set.seed(used.set.seed2)
backup.name <- c(backup.name, "used.set.seed2")
......@@ -941,7 +946,9 @@ if(random.seed == TRUE){
used.set.seed3 <- sample(x = 0:(2^31-1), size = 1)
}else{
used.set.seed3 <- 1
cat(paste0("\n\n================\n\nBEWARE: NON RANDOM set.seed(1) FUNCTION ACTIVATED \n\n================\n\n"))
tempo.cat <- paste0("\n\n================\n\nBEWARE: NON RANDOM set.seed(1) FUNCTION ACTIVATED \n\n================\n\n")
cat(tempo.cat)
fun_export_data(path = path.out, data = tempo.cat, output = log.file)
}
set.seed(used.set.seed3)
backup.name <- c(backup.name, "used.set.seed3")
......
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