summaryrefslogtreecommitdiff
path: root/Code/create_edges_mixtool.R
blob: 6ed852bb5294b948a3697d1a4c80f5cc96668da7 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
# 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])
k <- 2

####### 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)