args
length(args)
for(i in 1:length(args)){
eval(parse(text=args[[i]]))
}
infile <- "/Users/jvanheld/Documents/theses_et_memoires/Jaime_Castro/motif_clustering_scripts"
infile
infile
compare.matrices.table
test.Ncor
score
score
outfile <- "/Users/jvanheld/Documents/theses_et_memoires/Jaime_Castro/motif_clustering_scripts/peak-motifs_7nt_merged_oligos_positions_tree.json"
score.dist
score.dist
score
score
score.values
score.dist
test.Ncor
names(test.Ncor)
dist.values
compare.matrices.table
dist.matrix
im(dist.matrix)
dim(dist.matrix)
test.Ncor
test.Ncor - score.dist
compare.matrices.table
compare.matrices.table
matrix.names
matrix.names
matrix.dist
matrix.dist
compare.matrices.table[,2]
matrix.id1
j
j <- 2
i <- 1
)
matches
curent.sco
current.score
compare.matrices.table
compare.matrices.table[matches,°
compare.matrices.table[matches,score]
compare.matrices.table[matches,]
i
j
j <- 2
matches
compare.matrices.table[matches,]
compare.matrices.table[matches,score]
current.score
current.score
sum(matches)
which.mat
which(matches)
matches
length(matches)
which(matches)
matches[15]
current.score
matrix.dist
matrix.dist
length(matches)
dim(compare.matrices.table)
dim(matches)
matches
xtabs(2 ~1, compare.matrices.table)
xtabs(2 ~1, compare.matrices.table)
compare.matrices.table
xtabs(X.name1 ~ name2, compare.matrices.table)
xtabs(X.name1 ~ name2, as.matrix(compare.matrices.table))
xtabs(X.name1 ~ name2, as.matrix(compare.matrices.table))
xtabs(strand ~ name2, as.matrix(compare.matrices.table))
xtabs(strand ~ name2, as.matrix(compare.matrices.table))
xtabs("strand" ~ "name2", as.matrix(compare.matrices.table))
matrix.nb
matrix.nb^2
matrix.nb*matrix.nb
matrix.nb*(matrix.nb+1)/2
quit()
n
list(infile)
ls(infile)
infile
infile
list.files(infile)
list.files()
infile
description.file
system(paste("ls -ltr", description.file))
score.dist
dist.matrix
getwd
getwd()
getwd()
dev.off()
dev.off()
head(description.table)
attribtues(tree)
attributes(tree)
tee$order
tree$order
tree$merge
tree$order
tree$labels
tree$labels
tree$order
tree$merge
names(description.table)
tree$labels
matrix.labels
description.file
description.table
tree$labels
tree$merge
child1
child2
head(compare.matrices.table)
names(description.table)
head(description.table)
names(compare.matrices.table)
names(description.table)
names(description.table)
id1
child1
n1
id1
n1
n2
id1
id2
id1
compa.row
names(compare.matrices.table)
strand
strand
names(description.table)
compare.matrices.table)com
compa.nb
comp.nb
compa.nb
compare.matrices.table
compare.matrices.table[compa.nb,]
consensus
consensus1
consensus2
rep(x="H", n=10)
rep(x="H",times=10)
paste(rep(x="H",times=10))
paste(sep="",rep(x="H",times=10)))
paste(sep="",rep(x="H",times=10))
c(sep="",rep(x="H",times=10))
(sep="",rep(x="H",times=10))
paste(sep="",rep(x="H",times=10))
paste(collapse="",rep(x="H",times=10))
quit()
n
direct.interaction.table[, c("provider", "type", "detectionMethod")]
getwd()
dir.results
dir.results
system(paste("open", dir.results))
stats.per.provider
stats.per.provider
quit()
n
infile
demo.nb <- 1
## How to chance this path to make it general?
rsat.dir <- Sys.getenv("RSAT")
source(file.path(rsat.dir, "R-scripts", "cluster_motifs_lib.R"))
dir.demo <- file.path(rsat.dir, "public_html", "demo_files")
rsat.dir <- Sys.getenv("RSAT")
rsat.dir
rsat.dir <- Sys.getenv("RSAT")
rsat.dir
