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# Last modified 13 August 2019
TARGET_TF_FILE <- "../Data/information/target_tf.txt"
DATA_FILE <- "../Data/history/expr/TPM.txt" # A TPM table
AGINAME_FILE <- "../Data/information/AGI-to-gene-names_v2.txt"
CORR_THRESHOLD <- 0.5
MIN_SIZE <- 100
# Make sure we have required files
if (! file.exists(TARGET_TF_FILE)) {
stop(sprintf('[create_edges_mixtool.R] Unable to find %s', TARGET_TF_FILE))
}
if (! file.exists(DATA_FILE)) {
stop(sprintf('[create_edges_mixtool.R] Unable to find %s', DATA_FILE))
}
if (! file.exists(AGINAME_FILE)) {
stop(sprintf('[create_edges_mixtool.R] Unable to find %s', AGINAME_FILE))
}
###### get commandline arguments #########################
args <- commandArgs(trailingOnly=TRUE)
k <- strtoi(args[1])
####### Read data #########################################
X <- read.table(DATA_FILE, header=TRUE, check.names=FALSE)
gene_id <- X$gene_id
X$gene_id <- NULL
row.names(X) <- gene_id
X <- as.matrix(X)
rna.sample.id <- colnames(X)
target_tf <- read.table(TARGET_TF_FILE, sep='\t', header=FALSE)
target_tf <- as.matrix(target_tf)
#target_tf <- target_tf[nrow(target_tf):1,] # reverse rows
targets <- target_tf[,1]
tfs <- target_tf[,2]
conditions <- target_tf[,3]
agi <- read.table(AGINAME_FILE, stringsAsFactors=F) # AGINAME_FILE cannot contain quotes
#######################################################
library(mixtools)
options(max.print=999999999)
output.file <- paste('../Data/history/edges/one_target/edges.txt', 'mixtools', format(Sys.time(), '%b.%d.%Y.%H%M%S'), sep='.')
f <- file(output.file, 'w')
for (i in 1:length(targets)) {
curr.date <- gsub('-','',Sys.Date())
id1 <- tfs[i]
id2 <- targets[i]
if (id1 %in% gene_id == F || id2 %in% gene_id == F) {
next
}
name1 <- agi$V2[which(agi$V1 == id1)]
name2 <- agi$V2[which(agi$V1 == id2)]
cond <- conditions[i]
x <- X[id1,]
y <- X[id2,]
na.ratio <- max(sum(is.na(x))/length(x), sum(is.na(y))/length(y))
if (na.ratio > 0.5) {
next
}
x <- log(x+1)
y <- log(y+1)
sdx <- sd(x)
sdy <- sd(y)
index <- x < 0.01 | y < 0.01
x <- x[!index]
y <- y[!index]
if (length(x) < 20 || sdx < 0.25 || sdy < 0.5 ) {
print(i)
next
}
r <- cor(x, y)
if (abs(r) >= CORR_THRESHOLD) {
s = sprintf('%s %s\t%s %s\t%4.2f\t%s\t%s\t%s\t%s\t%s\n', id2, name2,id1,name1, r, 'all', '.', cond, '.', curr.date)
#cat(s, file=result.file, sep='\n', append=T)
#cat(s, sep='\n')
#flush.console()
#write.table(s, file.name, quote=F, sep='', row.names=F, append=T, col.names=F)
next
}
N <- length(x)
tryCatch( em.out <- regmixEM(y, x, maxit=100, epsilon=1e-03, k=k), error=function(e) NULL )
if (length(em.out) == 0) { # if there is an error when running regmixEM, we skip.
next
}
pos_r_max <- -2
pos_r_N <- 0
pos_r_index <- c()
pos_r_loglik <- -100000000
neg_r_max <- 2
neg_r_N <- 0
neg_r_index <- c()
neg_r_loglik <- -100000000
for (j in seq(1,k,1)) {
index <- which(max.col(em.out$posterior) == j)
size <- length(index)
r <- cor(em.out$x[index,2], em.out$y[index])
if (!is.na(r) && r >= CORR_THRESHOLD && size >= MIN_SIZE && r > pos_r_max && size > pos_r_N) {
pos_r_max <- r
pos_r_N <- size
pos_r_index <- index
pos_r_loglik <- em.out$loglik
}
if (!is.na(r) && r <= -CORR_THRESHOLD && size >= MIN_SIZE && r < neg_r_max && size > neg_r_N) {
neg_r_max <- r
neg_r_N <- size
neg_r_index <- index
neg_r_loglik <- em.out$loglik
}
}
if (pos_r_max > 0 && pos_r_loglik > -3000) {
sub.cond <- paste(rna.sample.id[pos_r_index], collapse=' ')
num.sub.cond <- length(rna.sample.id[pos_r_index])
s = sprintf('%s %s\t%s %s\t%4.2f\t%s\t%d\t%s\t%4.2f\t%s\t%4.2f\t%s\n', id2, name2, id1, name1, pos_r_max, 'mix', num.sub.cond, cond, pos_r_loglik, curr.date, pos_r_max, 'mixtool')
#cat(s, file=result.file, sep='\n', append=T)
#cat(s, sep='\n')
#write.table(s, file.name, quote=F, sep='', row.names=F, append=T, col.names=F)
cat(s, file=f, sep='')
}
if (neg_r_max < 0 && neg_r_loglik > -3000) {
sub.cond <- paste(rna.sample.id[neg_r_index], collapse=' ')
num.sub.cond <- length(rna.sample.id[neg_r_index])
s = sprintf('%s %s\t%s %s\t%4.2f\t%s\t%d\t%s\t%4.2f\t%s\t%4.2f\t%s\n', id2, name2, id1, name1, neg_r_max, 'mix', num.sub.cond, cond, neg_r_loglik, curr.date, neg_r_max, 'mixtool')
#cat(s, file=result.file, sep='\n', append=T)
#cat(s, sep='\n')
#write.table(s, file.name, quote=F, sep='', row.names=F, append=T, col.names=F)
cat(s, file=f, sep='')
}
cat('', file=f, sep='')
}
close(f)
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