Ns126:Calendar/NOTES/2015-4-21: Difference between revisions
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print(c((c1),(c2),Pair=c3)) | print(c((c1),(c2),Pair=c3)) | ||
} | } | ||
{| class="wikitable" style="text-align: right; color: red;" | |||
| ||Cancer||Normal||Paired||Total | |||
|- | |||
| COAD||312||38||76||350 | |||
|- | |||
| LUAD||473||32||58||505 | |||
|- | |||
| LUSC||370||42||80||412 | |||
|- | |||
| PAAD||184||10||20||194 | |||
|- | |||
| | |||
|- | |||
|} |
Revision as of 22:28, 21 April 2015
- Now, I do know how to insert figures, but I don't know how to insert tables into MediaWiki. Therefore, I write a small code to transfer routine table to wikitable.
- I must say: mediawiki is really a excellent tool to manage the lab and monitor the progress or task to help us complete the project quickly.
perl table2wikitable.pl input.table.txt
#!/usr/bin/perl #table2wikitable.pl use strict; use Cwd; chdir getcwd; my $input=@ARGV[0]; open F,$input; print "{| class=\"wikitable\" style=\"text-align: right; color: red;\"\n"; while(<F>){ chomp; my @line=split /\t/; my $tmp=join("||",@line); print "| $tmp\n|-\n"; } print"|}\n";
- corresponding table is as the following. Pan-Cancer Methylation 450K dataset were collected from TCGA Project to identify optional padloc regions.
Symbol | Case | Control | Cancer | 肿瘤名称 |
KIRC | 160 | 160 | Kidney renal clear cell carcinoma | 肾透明细胞癌 |
BRCA | 92 | 92 | Breast invasive carcinoma | 浸润性乳腺癌 |
THCA | 56 | 56 | Thyroid carcinoma | 甲状腺癌 |
HNSC | 50 | 50 | Head and Neck squamous cell carcinoma | 头颈部鳞状细胞癌 |
PRAD | 49 | 49 | Prostate adenocarcinoma | 前列腺癌 |
LIHC | 49 | 49 | Liver hepatocellular carcinoma | 肝癌 |
KIRP | 45 | 45 | Kidney renal papillary cell carcinoma | 肾乳头状细胞癌 |
LUSC | 41 | 41 | Lung squamous cell carcinoma | 肺腺癌 |
COAD | 39 | 39 | Colon adenocarcinoma | 结肠癌 |
UCEC | 30 | 30 | Uterine Corpus Endometrial carcinoma | 子宫内膜癌 |
LUAD | 26 | 26 | Lung adenocarcinoma | 肺鳞癌 |
- In order to publish MONOD paper to a good paper quickly. 1) fast 2) large data
- collect methylation 450 data of cancer tissues and normals from TCGA Project
- sample size
- clinical information: gender, age
- collect methylation 450 data of cancer tissues and normals from TCGA Project
tar xvf 08177614-f305-4fbf-84ca-fd2fbfe26755.tar # tar xvf 548dd1cf-84a1-4d96-86f0-b47d6300daa6.tar # tar xvf 9cd95b1c-782c-478d-9ec9-de7c9c441cc4.tar # tar xvf c5da6cd3-0266-4ebb-bd11-713ffe9b5ef9.tar #
- focus on 3 cancers which we have preliminary data (lung, colon, pancreatic)
library("stringr") for(cancer in c("COAD","LUAD","LUSC","PAAD")){ dir<-paste("/home/sguo/monod/data/",tolower(cancer),"/DNA_Methylation/JHU_USC__HumanMethylation450/Level_3",sep="") setwd(dir) pattern=paste("jhu-usc.edu_",cancer,".*",sep="") print (pattern) file=list.files(pattern=pattern) idv<-unique(as.array(str_extract(file,"TCGA-[0-9|a-z|A-Z]*-[0-9|a-z|A-Z]*"))) pairidv<-c() for (i in 1:length(idv)){ t1<-paste(idv[i],"-01",sep="") t2<-paste(idv[i],"-11",sep="") if(all(any(grepl(t1,file)),any(grepl(t2,file)))){ pairidv<-c(pairidv,t1,t2) } } l1<-length(pairidv) l2<-length(file) id1<-lapply(lapply(strsplit(file,"[.]"),function(x) x[6]),function(x) substr(x,1,15)) id2<-lapply(lapply(strsplit(file,"[.]"),function(x) x[6]),function(x) substr(x,14,15)) sam<-lapply(lapply(strsplit(file,"[.]"),function(x) x[6]),function(x) substr(x,1,15)) tab<-table(unlist(lapply(lapply(strsplit(file,"[.]"),function(x) x[6]),function(x) substr(x,14,15)))) c1<-tab[which(names(tab)=="01")] c2<-tab[which(names(tab)=="11")] c3<-length(pairidv) print(c((c1),(c2),Pair=c3)) }
Cancer | Normal | Paired | Total | |
COAD | 312 | 38 | 76 | 350 |
LUAD | 473 | 32 | 58 | 505 |
LUSC | 370 | 42 | 80 | 412 |
PAAD | 184 | 10 | 20 | 194 |