# personal notes
library(VennDiagram)
data=list(A=c(1,2,3,4,5,6),B=c(3,4,5,6,7),C=c(5,6,7,8,9,10)) # demo data
venn.diagram(data,”vennFigure.tiff”,fill = c(“cornflowerblue”, “green”, “yellow”)) # venn diagram saved to a file
# for personal notes
@group=(0,1,2,3,4);
# generate files and file handles
foreach $i (@group){
$train[$i]=”train_$i.txt”; # file name
$FILE[$i]=”FILE”.”$i”; # file handle
open $FILE[$i],”>$train[$i]” or die;
}
# write to file
foreach $i (@group){
print {$FILE[$i]} “test\n”;
close $FILE[$i];
}
# R code for convert gene/transcripts names
# personal notes
require(biomaRt)
# settings
features=c(“ensembl_gene_id”,”ensembl_transcript_id”,”entrezgene”,”external_gene_name”,”refseq_mrna”)
host=”www.ensembl.org”
# human
human_file=”geneID_mapping_human.tsv”
hmart=useMart(“ENSEMBL_MART_ENSEMBL”, dataset=”hsapiens_gene_ensembl”,host=host)
results=getBM(attributes=features,mart=hmart)
write.table(results,human_file,sep=”\t”,quote=FALSE,row.names=FALSE,col.names=TRUE)
# mouse
mouse_file=”geneID_mapping_mouse.tsv”
mmart=useMart(“ENSEMBL_MART_ENSEMBL”, dataset=”mmusculus_gene_ensembl”,host=host)
results=getBM(attributes=features,mart=mmart)
write.table(results,mouse_file,sep=”\t”,quote=FALSE,row.names=FALSE,col.names=TRUE)