-
Notifications
You must be signed in to change notification settings - Fork 0
/
sva_scale.r
executable file
·101 lines (62 loc) · 2.19 KB
/
sva_scale.r
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
require(sva)
require(ggplot2)
# require(affy)
# require(affydata)
t1 = read.csv('survival/clinical.info.data.frame.txt',header = T,row.names = 1,stringsAsFactors = FALSE,sep='')
t2 = read.csv('D:/R_workspace/survival/expr_data.csv',row.names = 1)
t2 = as.matrix(t2)
t1$gender[which(t1$gender=='F')]=1
t1$gender[which(t1$gender=='M')]=2
t1$gender = as.integer(t1$gender)
# combat
batch = t1$sequencing.protocol
batch[batch=='anchordx'] = 1
batch[batch=='novogene'] = 2
modcombat = model.matrix(~1, data = t1)
combat_edata = ComBat(dat=t2, batch=batch, mod=modcombat, par.prior=TRUE, prior.plots=TRUE)
mod = model.matrix(~as.factor(cencor.status), data=t1)
mod0 = model.matrix(~1, data = t1)
pValuesComBat = f.pvalue(combat_edata,mod,mod0)
qValuesComBat = p.adjust(pValuesComBat,method="BH")
pValuesComBat_005 = pValuesComBat[pValuesComBat<0.05]
pValuesComBat_005 = rownames(data.frame(pValuesComBat_005))
sample_data = as.data.frame(t(combat_edata))
pv = sample_data[pValuesComBat_005]
pv$gender = t1$gender
x = as.matrix(pv)
y = t1$survival.month
#########################
col_batch = batch
col_batch[col_batch==1] = 'brown1'
col_batch[col_batch==2] = 'green'
#normal_data
bef_data = as.data.frame(t2)
bef_data[bef_data==0]=NA
boxplot(bef_data)
#combat_data
aft_data = combat_edata
aft_data[aft_data==0]=NA
#median——scale
j2 = log(aft_data)
mean_median = mean(apply(aft_data,2,median,na.rm = TRUE),na.rm = TRUE)
scale_median_2 <- function(df){
a = median(df,na.rm = TRUE)
b = sd(df,na.rm = TRUE)
c = (df-a+mean_median)/b
return(c)
}
scale_median_combat = apply(j2,2,scale_median_2)
# png("survival/data_expr//combat_scale.png",width = 2560,height = 1440)
par(mfrow = c(3,1))
par(cex=1.2)
boxplot(log(bef_data),col=c(col_batch),main="original_data")
boxplot(log(aft_data),col=c(col_batch),main="combat_data")
boxplot(scale_median_combat,col=c(col_batch),main="scale_median")
# dev.off()
scale_median_3 <- function(df){
a = median(df,na.rm = TRUE)
c = (df-a+mean_median)
return(c)
}
scale_median_data = apply(aft_data,2,scale_median_3)
a11 = apply(scale_median_data,2,median,na.rm = TRUE)