-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathMethylation_SCC_vs_Adeno_2_SCC.R
154 lines (138 loc) · 5.64 KB
/
Methylation_SCC_vs_Adeno_2_SCC.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
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
###given symbol : symbol(s) in file
###ACP5: ACP5
###C2orf32: CRIP1
###CCDC50: CCDC50 CCDC50;UTS2D UTS2D;CCDC50
###CPEB1: CPEB1
###CST6: CST6
###DKK3: DKK3
###GJB2: GJB2
###GSTT2: GSTT2B;GSTT2 GSTT2:GSTT2B DTT;GSTT2 GSTT2;DTT
###HTRA3: HTRA3
###HTRA4: HTRA4 HTRA4;PLEKHA2 PLEKHA2;HTRA4
###IGDCC4 (NOPE): IGDCC4
###LAYN: LAYN
###LOX: LOX
###MARVELD3: MARVELD3
###MSX1: MSX1
###MT1M: MT1M
###PAK6-2: PAK6;C15orf56 C15orf56;PAK6
###(Note: the gene is PAK6 but the methylated CpG island is the one in the middle of the gene that is close to the TSS for the smaller transcripts. Only the probes corresponding to this spot were considered, with corresponding gene symbol PAK6;C15orf56. See http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr15:40509629-40569688&hgsid=338380169&knownGene=full)
###RBP1: RBP1
###ROBO3: ROBO3
###TMEM22: TMEM22
###TPM1: TPM1
###ZNF365: ZNF365
###BNIP3: BNIP3
###EMILIN2: EMILIN2
###MSRB3: MSRB3
###VAV3: VAV3
###AKAP12: AKAP12
###SYNE1: SYNE1
###IL20R: IL20RA
###p16: CDKN2A CDKN2A;CDKN2BAS CDKN2BAS;CDKN2A
###RASSF1A: RASSF1 RASSF1;ZMYND10 ZMYND10;RASSF1
###MGMT-O6: MGMT
###SFRP2: SFRP2
###SFRP1: SFRP1
###BETA3, BHLHB5: BHLHE22, BHLHE22;LOC401463 LOC401463;BHLHE22
###NOVEL2: TOX2
###IGFBP3: IGFBP3
###Reprimo (RPRM): RPRM
###DCR1: TNFRSF10C
###HLHP: BHLHE41
###AK5: AK5
###TSLC1: CADM1
###TUBB4: TUBB4 MIR220B;TUBB4 TUBB4;MIR220B
###XT3: SLC6A20
###PCDH10: PCDH10
###MMP2: MMP2
###APC2: APC2
###GPNMB: GPNMB
###BOLL: BOLL
###ICAM5: ICAM5 ICAM5;ICAM4
###JPH3: JPH3
###GNB4: GNB4
###SYNE1: SYNE1
setwd("Z:/Leng/LUSC/LUSC.HumanMethylation450.Level_3")
filenames=list.files()
file1=read.table(filenames[1],sep="\t",header=T,skip=1)
dimnames(file1)[[2]]
x=table(file1$Gene_Symbol)
idx1=which(file1$Gene_Symbol=="ACP5")
idx2=which(file1$Gene_Symbol=="CRIP1")
idx3=which(file1$Gene_Symbol=="CCDC50" | file1$Gene_Symbol=="CCDC50;UTS2D" | file1$Gene_Symbol=="UTS2D;CCDC50")
idx4=which(file1$Gene_Symbol=="CPEB1")
idx5=which(file1$Gene_Symbol=="CST6")
idx6=which(file1$Gene_Symbol=="DKK3")
idx7=which(file1$Gene_Symbol=="GJB2")
idx8=which(file1$Gene_Symbol=="GSTT2B;GSTT2" | file1$Gene_Symbol=="GSTT2:GSTT2B")
idx9=which(file1$Gene_Symbol=="HTRA3")
idx10=which(file1$Gene_Symbol=="HTRA4" | file1$Gene_Symbol=="HTRA4;PLEKHA2" | file1$Gene_Symbol=="PLEKHA2;HTRA4")
idx11=which(file1$Gene_Symbol=="IGDCC4")
idx12=which(file1$Gene_Symbol=="LAYN")
idx13=which(file1$Gene_Symbol=="LOX")
idx14=which(file1$Gene_Symbol=="MARVELD3")
idx15=which(file1$Gene_Symbol=="MSX1")
idx16=which(file1$Gene_Symbol=="MT1M")
idx17=which(file1$Gene_Symbol=="PAK6;C15orf56" | file1$Gene_Symbol=="C15orf56;PAK6" )
idx18=which(file1$Gene_Symbol=="RBP1")
idx19=which(file1$Gene_Symbol=="ROBO3")
idx20=which(file1$Gene_Symbol=="TMEM22")
idx21=which(file1$Gene_Symbol=="TPM1")
idx22=which(file1$Gene_Symbol=="ZNF365")
idx23=which(file1$Gene_Symbol=="BNIP3")
idx24=which(file1$Gene_Symbol=="EMILIN2")
idx25=which(file1$Gene_Symbol=="MSRB3")
idx26=which(file1$Gene_Symbol=="VAV3")
idx27=which(file1$Gene_Symbol=="AKAP12")
idx28=which(file1$Gene_Symbol=="SYNE1")
idx29=which(file1$Gene_Symbol=="IL20RA")
idx30=which(file1$Gene_Symbol=="CDKN2A" | file1$Gene_Symbol=="CDKN2A;CDKN2BAS" | file1$Gene_Symbol=="CDKN2BAS;CDKN2A")
idx31=which(file1$Gene_Symbol=="RASSF1" | file1$Gene_Symbol=="RASSF1;ZYMND10" | file1$Gene_Symbol=="ZYMND10;RASSF1")
idx32=which(file1$Gene_Symbol=="MGMT")
idx33=which(file1$Gene_Symbol=="SFRP2")
idx34=which(file1$Gene_Symbol=="SFRP1")
idx35=which(file1$Gene_Symbol=="BHLHE22" | file1$Gene_Symbol=="BHLHE22;LOC401463" | file1$Gene_Symbol=="LOC401463;BHLHE22")
idx36=which(file1$Gene_Symbol=="TOX2")
idx37=which(file1$Gene_Symbol=="IGFBP3")
idx38=which(file1$Gene_Symbol=="RPRM")
idx39=which(file1$Gene_Symbol=="TNFRSF10C")
idx40=which(file1$Gene_Symbol=="BHLHE41")
idx41=which(file1$Gene_Symbol=="AK5")
idx42=which(file1$Gene_Symbol=="CADM1")
idx43=which(file1$Gene_Symbol=="TUBB4" | file1$Gene_Symbol=="MIR220B;TUBB4" | file1$Gene_Symbol=="TUBB4;MIR220B")
idx44=which(file1$Gene_Symbol=="SLC6A20")
idx45=which(file1$Gene_Symbol=="PCDH10")
idx46=which(file1$Gene_Symbol=="MMP2")
idx47=which(file1$Gene_Symbol=="APC2")
idx48=which(file1$Gene_Symbol=="GPNMB")
idx49=which(file1$Gene_Symbol=="BOLL")
idx50=which(file1$Gene_Symbol=="ICAM5" | file1$Gene_Symbol=="ICAM5;ICAM4" | file1$Gene_Symbol=="ICAM4;ICAM5")
idx51=which(file1$Gene_Symbol=="JPH3")
idx52=which(file1$Gene_Symbol=="GNB4")
idx53=which(file1$Gene_Symbol=="SYNE1")
idx.all <- c(idx1, idx2, idx3, idx4, idx5, idx6, idx7, idx8, idx9,
idx10, idx11, idx12, idx13, idx14, idx15, idx16, idx17, idx18, idx19,
idx20, idx21, idx22, idx23, idx24, idx25, idx26, idx27, idx28, idx29,
idx30, idx31, idx32, idx33, idx34, idx35, idx36, idx37, idx38, idx39,
idx40, idx41, idx42, idx43, idx44, idx45, idx46, idx47, idx48, idx49,
idx50, idx51, idx52, idx53)
Extract1=t(file1[idx.all,c(1,3,2)])
#6/5/2013: changed below from dimnames to row.names for my own ease of understanding (Phil)
row.names(Extract1)<-c("probe.name","Gene_Symbol",as.character(filenames[1]))
data=NULL
data=rbind(data,Extract1)
#added timer to determine run time of for loop
ptm <- proc.time()
for (i in c(2:length(filenames))){
file=read.table(filenames[i],sep="\t",header=T,skip=1)
trans.file=t(file[idx.all,2])
row.names(trans.file) <- as.character(filenames[i])
data=rbind(data,trans.file)
}
#end timer
proc.time() - ptm
write.csv(data,"Z:/Leng/Phil/Methylation_SCC_vs_Adeno_2/output/Methylation450K_TCGA_SCCvsAdeno_2_SCC_1.csv")
#proc.time() - ptm
#user system elapsed
#1826.30 28.83 2220.77