Modify configuration file loading in R scripts to avoid character str…

…ings being loaded as factors, following #24
lentendu · Mar 7, 2024 · a67dc5d · a67dc5d
1 parent 76cbeb1
commit a67dc5d
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Showing 8 changed files with 8 additions and 8 deletions.
diff --git a/rscripts/clean_mat.R b/rscripts/clean_mat.R
@@ -10,7 +10,7 @@ suppressMessages(library(doParallel))
 suppressMessages(library(compositions))
 
 # read options
-config<-read.table("config",h=T,as.is=2)
+config<-read.table("config",h=T,colClasses=c(cksum="character",mat="character"))
 mat<-read.table(config$mat,h=T)
 write(nrow(mat),"nbsamp_ori")
 write(ncol(mat),"nbotu_ori")

diff --git a/rscripts/edges_p.R b/rscripts/edges_p.R
@@ -5,7 +5,7 @@ suppressMessages(library(rhdf5))
 block<-as.numeric(commandArgs()[7])
 
 # read options
-config<-read.table("config",h=T,as.is=2)
+config<-read.table("config",h=T,colClasses=c(cksum="character",mat="character"))
 for (i in 4:ncol(config)){assign(names(config)[i],config[1,i])}
 
 # get p.values of edges above threshold (one block at a time)

diff --git a/rscripts/edges_p_ex.R b/rscripts/edges_p_ex.R
@@ -5,7 +5,7 @@ suppressMessages(library(rhdf5))
 block<-as.numeric(commandArgs()[7])
 
 # read options
-config<-read.table("config",h=T,as.is=2)
+config<-read.table("config",h=T,colClasses=c(cksum="character",mat="character"))
 for (i in 4:ncol(config)){assign(names(config)[i],config[1,i])}
 
 # get p.values of edges above threshold

diff --git a/rscripts/edges_r.R b/rscripts/edges_r.R
@@ -7,7 +7,7 @@ threshold<-scan("threshold",quiet=T)
 threshold_ex<-scan("ex_threshold",quiet=T)
 
 # read options
-config<-read.table("config",h=T,as.is=2)
+config<-read.table("config",h=T,colClasses=c(cksum="character",mat="character"))
 for (i in 4:ncol(config)){assign(names(config)[i],config[1,i])}
 
 # Read Spearman's rho from noise added matrix (one block at a time)

diff --git a/rscripts/network.R b/rscripts/network.R
@@ -8,7 +8,7 @@ ncores<-as.numeric(commandArgs()[7])
 blocks<-as.numeric(commandArgs()[8])
 
 # read options
-config<-read.table("config",h=T,as.is=2)
+config<-read.table("config",h=T,colClasses=c(cksum="character",mat="character"))
 for (i in 4:ncol(config)){assign(names(config)[i],config[1,i])}
 
 # load edges

diff --git a/rscripts/rand_network.R b/rscripts/rand_network.R
@@ -7,7 +7,7 @@ suppressMessages(library(igraph,quietly=T))
 seed<-as.numeric(commandArgs()[7])
 
 # Read options
-config<-read.table("config",h=T,as.is=1)
+config<-read.table("config",h=T,colClasses=c(cksum="character",mat="character"))
 for (i in 4:ncol(config)){assign(names(config)[i],config[1,i])}
 
 # load normalize matrix 

diff --git a/rscripts/spearman.R b/rscripts/spearman.R
@@ -5,7 +5,7 @@ suppressMessages(library(rhdf5))
 seed<-as.numeric(commandArgs()[7])
 
 # read options
-config<-read.table("config",h=T,as.is=2)
+config<-read.table("config",h=T,colClasses=c(cksum="character",mat="character"))
 
 # load normalize matrix
 mat<-readRDS("mat")

diff --git a/rscripts/threshold_range.R b/rscripts/threshold_range.R
@@ -5,7 +5,7 @@ suppressMessages(library(igraph,quietly=T))
 suppressMessages(library(rhdf5))
 
 # read options
-config<-read.table("config",h=T,as.is=2)
+config<-read.table("config",h=T,colClasses=c(cksum="character",mat="character"))
 for (i in 4:ncol(config)){assign(names(config)[i],config[1,i])}
 
 # load normalize matrix